Building mocoLUFA under OSX & Linux
This is Franco, from Yaeltex, the guys who put up that site for custom MocoLUFA compiling.

Our site works on an Ubuntu server, and the build environment can be seen at the bottom of the site, which is as follows:


Ubuntu Server Setup


avr-gcc: avr-gcc (GCC) 4.9.2
avrdude: Version 6.3, compiled on Mar 15 2016 at 21:26:45
LUFA: 100807
dualMocoLUFA: custom Yaeltex based on 2013/09/22



On the other hand, I use Windows 10 to build locally in my computer, and I have a similar setup with sligthly older versions of avr-gcc and avrdude:


Windows 10 Server Setup


avr-gcc: avr-gcc (GCC) 4.3.3
avrdude: Version 5.10, compiled on Mar 15 2016 at 21:26:45
LUFA: 100807
dualMocoLUFA: custom Yaeltex based on 2013/09/22



Here is a link to the fork we made to mocoLUFA, it has minor changes, that were very useful to us and our hardware.

Regarding your problem, I am really lost on the cause of it, but we can start with some questions to get closer to a solution.


What kind of MIDI messages are you trying to send/receive?
Can you share the code you are using?
Are you using Arduino MIDI Library (Last version is v4.3.1)?
If not, are you sure you are using 31.250 bps as baud rate?
Do you have something else connected to TX or RX lines in your circuit?


Let's start with these. Cheers!