Vag-Com and NefMoto both use the communication protocols to communicate with the code on the ECU. Boot mode uses the communication systems built into the ROM of the processor.
If you cannot connect with Vag-Com or NefMoto, but can connect with boot mode, then likely the ECU code in the flash memory chip is corrupt and preventing the ECU from booting properly.
thanks tony, do you know what chip location is the flash memory?