Here is a reasonable explanation of the function of decoupling capacitors. 100nF is a pretty typical value for decoupling caps and there should be one for each VCC/AVCC pin. They should to be placed as physically close to the VCC/AVCC pins as possible.
Hmmm, well the weird thing is that the original Micro has just 2 caps for all the VCC/AVCC pins.
Well the problem is the PCBs are already made, so it will probably take a while until I have the time to fix the files and order a new batch.
Also had the board running the USB serial test sketch for at least an hour and the connection had no problem, also it seems like there is almost no Unknown Device problems while it is programmed with that sketch.
Oscar