I have the same problem. Uploading a program via USB gives me timeout error on Mega2560.
I found one workaround for this.
When I burn bootloader with ISP programmer, I can upload sketch via USB only 1 time. When uploading second time, I get timeout. Then I take my ISP programmer and burn Mega2560 new bootloader. Then I can upload sketch once again.
Fu**ing annoying.