I've never seen something similar.
How is the connection from Rx/Tx to your PC made? Level shifter?
Is it possible for you to post your complete project, so that we all can have a look at all of your settings? To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
Further investigation shows it is the 25ms worth of blocking adc/eeprom action right after the Timer Interrupt that breaks the UART communication.
Also, my exampe USB_UART code was written polling, so mine is polling instead of interrupt driven.
I'll need to investigate changing that.
I am not quite sure, but I remember that during eeprom write clocks are changed.
25ms in an interrupt handler is a very long time