Hello,
On AVR-CDC site "http://www.recursion.jp/avrcdc/", they add two diodes to operating the AVR at 3.6 Volts.
"The Vcc should be lower than 3.6V to avoid SYNC errors."
On this site : "http://www.obdev.at/products/avrusb/index.html" :
"D1 and D2 are a low cost relpacement for a low drop 3.3 V regulator chip. Operating the AVR at higher voltages exceeds the common mode range of many USB chips. If you need to run the AVR at 5 V, add 3.6 V zener diodes at D+ and D- to limit the voltage."
Why don't you do that on your project ?
Thanks.