AVR ISP MKII program atmega2560 with 16u2/32u4 problems

[Nevada Smith]

Hi,
I got the AVR ISP MKII working with windows and the Arduino software.

What i did:
Changed one line in the makefile:
CC_FLAGS     = -DUSE_LUFA_CONFIG_HEADER -DLIBUSB_DRIVER_COMPAT -DNO_VTARGET_DETECT -IConfig/
Changed mcu to atmega16u2 or 32u4.
Installed the libusb driver because the atmel studio driver doesnt work under windows.
http://sourceforge.net/projects/libusb-win32/?source=navbar

All files are attached to this post!

So i uploaded the hex files to each chip. The 16u2 on the Arduino Mega (via dfu), the 32u4 on the Arduino Pro Micro (the 32u4 hex with the 16u2 and the burn bootloader function actually).
So i can reprogram my Pro mino (328p) with both chips and the arduino ide 1.0.5 perfectly. Also programming a 32u4 works fine. I can upload sketches and burn bootloaders.

I found 3 problems:
I cannot burn bootloaders with the 1.5.6 ide, the device will disconnect then. Uploading sketches works fine.
I cannot burn bootloaders or normal sketches with 1.5.7 ide. Not sure if this is an Arduino or Lufa bug. Want to note this here. Ide 1.0.5 works fine.
The main problem: I can program the mega2560 chip with the 32u4 without problems (reset pin is 8 on pro micro, PB4 i think). But the 16u2 just cant do it. It say uploading... and stays like this.

Any idea why this happens? Does the 16u2 has to small ram (500b) or maybe another error? What about the new ide errors?