Error uploading Arduino Micro Sketch using Kubuntu
Therefore I tried the newest version of the Arduino software from the arduino homepage.
  
  The package version I am using is 1:1.0.5+dfsg2-2, the other I tried was 2:1.0.5+dfsg2-4. 


That is not the newest version.

I think the more recent versions of the IDE are more robust - after all they have fixed reported bugs. Try 1.6.5 or 1.6.7. The version 1.0.5 is pretty old.



I too have had "upload completed" on my Leonardo (virtually the same as the Micro) when it did no such thing.

I am using Ubuntu 14.04 and don't have any problems programming my Micro with IDE 1.6.7.



When programming you should see the Tx/Rx and yellow LEDs flicker. If not, press Reset when it starts to upload and try again.



Have you followed the instructions here? Arduino Troubleshooting.




  I installed the arduino software using apt-get ...


Personally I download the IDE from this page: https://www.arduino.cc/en/Main/Software



Update

I just compiled and uploaded "Blink" with IDE 1.6.7 to my Micro on Ubuntu 14.04. This is what I saw:

Forcing reset using 1200bps open/close on port /dev/ttyACM1
PORTS {/dev/ttyACM0, /dev/ttyACM1, } / {/dev/ttyACM0, } =&gt; {}
PORTS {/dev/ttyACM0, } / {/dev/ttyACM0, /dev/ttyACM1, } =&gt; {/dev/ttyACM1, }
Found upload port: /dev/ttyACM1
/home/nick/Development/arduino-1.6.7/hardware/tools/avr/bin/avrdude -C/home/nick/Development/arduino-1.6.7/hardware/tools/avr/etc/avrdude.conf -v -patmega32u4 -cavr109 -P/dev/ttyACM1 -b57600 -D -Uflash:w:/tmp/build8f287ac41038dd4edf2d64ea95be7b6f.tmp/Blink.ino.hex:i 

avrdude: Version 6.0.1, compiled on Apr 14 2015 at 19:04:16
         Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
         Copyright (c) 2007-2009 Joerg Wunsch

         System wide configuration file is "/home/nick/Development/arduino-1.6.7/hardware/tools/avr/etc/avrdude.conf"
         User configuration file is "/home/nick/.avrduderc"
         User configuration file does not exist or is not a regular file, skipping

         Using Port                    : /dev/ttyACM1
         Using Programmer              : avr109
         Overriding Baud Rate          : 57600
         AVR Part                      : ATmega32U4
         Chip Erase delay              : 9000 us
         PAGEL                         : PD7
         BS2                           : PA0
         RESET disposition             : dedicated
         RETRY pulse                   : SCK
         serial program mode           : yes
         parallel program mode         : yes
         Timeout                       : 200
         StabDelay                     : 100
         CmdexeDelay                   : 25
         SyncLoops                     : 32
         ByteDelay                     : 0
         PollIndex                     : 3
         PollValue                     : 0x53
         Memory Detail                 :

                                  Block Poll               Page                       Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  MaxW   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ----- ---------
           eeprom        65    20     4    0 no       1024    4      0  9000  9000 0x00 0x00
           flash         65     6   128    0 yes     32768  128    256  4500  4500 0x00 0x00
           lfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           hfuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           efuse          0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           lock           0     0     0    0 no          1    0      0  9000  9000 0x00 0x00
           calibration    0     0     0    0 no          1    0      0     0     0 0x00 0x00
           signature      0     0     0    0 no          3    0      0     0     0 0x00 0x00

         Programmer Type : butterfly
         Description     : Atmel AppNote AVR109 Boot Loader

Connecting to programmer: .
Found programmer: Id = "CATERIN"; type = S
    Software Version = 1.0; No Hardware Version given.
Programmer supports auto addr increment.
Programmer supports buffered memory access with buffersize=128 bytes.

Programmer supports the following devices:
    Device code: 0x44

avrdude: devcode selected: 0x44
avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x1e9587
avrdude: reading input file "/tmp/build8f287ac41038dd4edf2d64ea95be7b6f.tmp/Blink.ino.hex"
avrdude: writing flash (4456 bytes):

Writing | ################################################## | 100% 0.33s

avrdude: 4456 bytes of flash written
avrdude: verifying flash memory against /tmp/build8f287ac41038dd4edf2d64ea95be7b6f.tmp/Blink.ino.hex:
avrdude: load data flash data from input file /tmp/build8f287ac41038dd4edf2d64ea95be7b6f.tmp/Blink.ino.hex:
avrdude: input file /tmp/build8f287ac41038dd4edf2d64ea95be7b6f.tmp/Blink.ino.hex contains 4456 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 0.03s

avrdude: verifying ...
avrdude: 4456 bytes of flash verified

avrdude done.  Thank you.


Can you please compare to what you get? Or post exactly what you see?



What do you see in your Port menu? This is what I see:





Installing Arduino on a fresh Ubuntu system

I did the following steps to get Arduino up on Ubuntu 14.04, on a PC where it was not previously installed.

Download and install


Downloaded Linux IDE 1.6.7 (64 bit) from https://www.arduino.cc/en/Main/Software
Un-archive downloaded file into ~/development folder
Executed from terminal:  ./arduino


Compile "blink"


Selected Uno device type
Loaded "Blink" from examples
Uploaded (checked Uno showed in menu as shown above)
Got error:

Sketch uses 1,030 bytes (3%) of program storage space. Maximum is 32,256 bytes.
Global variables use 9 bytes (0%) of dynamic memory, leaving 2,039 bytes for local variables. Maximum is 2,048 bytes.
avrdude: ser_open(): can't open device "/dev/ttyACM0": Permission denied
ioctl("TIOCMGET"): Inappropriate ioctl for device



Check permissions, join dialout and tty groups

See owner of /dev/ttyACM*

$ ls -l /dev/ttyACM*
crw-rw---- 1 root dialout 166, 0 Feb  1 07:32 /dev/ttyACM0


Am I in that group? (No)

getent group dialout
dialout:x:20:


Add to group dialout:

$ sudo usermod -a -G dialout nick


Am I in that group? (Yes)

$ getent group dialout
dialout:x:20:nick


Try again:

avrdude: ser_open(): can't open device "/dev/ttyACM0": Permission denied
ioctl("TIOCMGET"): Inappropriate ioctl for device
Problem uploading to board.  See http://www.arduino.cc/en/Guide/Troubleshooting#upload for suggestions.


Add to group tty:

$ sudo usermod -a -G tty nick


Check groups I am in:

$ groups nick
nick : nick adm tty dialout cdrom sudo dip plugdev lpadmin sambashare


Try again (same error).

Log out and log back in

After logging out and back in, it uploaded OK! Changed to Micro board (very similar to Leonardo) - still uploaded OK (after changing board type in IDE).

Check USB for Micro

After reset:

$ lsusb | grep Arduino
Bus 002 Device 014: ID 2341:0036 Arduino SA 


After about 3 seconds:

$ lsusb | grep Arduino
Bus 002 Device 015: ID 2341:8037 Arduino SA