Windows stops recognizing Arduinos
After a couple of hours I figured out what was happening so I will write all my analysis here for anyone having some of my problems.

First, a list of my components:

-USB TTL ship, used to upload programs to Arduino Pro. The one on the picture on instructables dot com /id/Usb-to-SerialTTL-adapter/, and used that driver.

-Arduino Pro. Chinese copy, red board just like Sparkfun's. 328p chip @ 5V = 16mhz.

-A board very similar to this one. It has a chip with FT232 written on it, also FTDI in bold letters.


The big USB TTL pcb I was using has 5 output pins: 3v3, 5v, TX, RX, GND. Turns out this is not enough to program Arduino Pro as you need one more pin. If you don't connect this pin, avrdude just gets stuck after opening the COM port and waits indefinitely/until you kill the process. To even be able to see this USB TTL chip in Windows, you need to download a driver from the website(first link) and my guess is that the driver is buggy since it won't exit the process when it encounters this type of error, further leading to suspicious/dangerous behaviour which results in Windows completely shutting down all COM ports until next restart. 

To get this pin(it's called DTR/GRN), I borrowed the other chip(3rd) and I connected it regarding to this scheme: 

I also had to download a different driver for it, I don't remember where I downloaded it from but it's called CDM21226 driver, when you install it it says FTDI driver installed. 

Now my uploading was getting stuck no more, however after the first successful upload to my Arduino Pro the upload process would get stuck in the part where it is burning the program, if you turn verbose option in Arduino IDE on, you can see something like Writing: [#######              ].

It turns out this driver was faulty too, as I uninstalled it and when I installed it with the very same setup as before it worked seamlessly ever since. It also took me some time how to uninstall a Windows driver without using Device Manager because it wouldn't show up there - no device attached to it.

To do that open Command Prompt as admin and type pnputil.exe -e to get a list of all drivers. Among them will be one called FTDI and that's the guy, in my case he was called oem51.inf. To delete him, type pnputil.exe -d oem51.inf, or add -f before -d to force deletion - in my case it kept saying device is busy so it required this drastic measure. Change 51 to the number you have above your ftdi driver. After this just install the driver again and everything should be fine, even without reboot.

Phew...
So much work to get a simple program burned to Arduino Pro. Hope you have less trouble with it than I did.