Arduino Mega - Upload problem with bootloader

Hi,
since a few days I can not upload programs to my Mega R3 over USB using the bootloader. The debug message from avrdude is avrdude: stk500v2_ReceiveMessage(): timeout. I can't remember that I changed anything.
Upload of programs with ISP is working fine. Communication over serial (USB) is fine (Loopback test and from programs).
The board gets a reset, when starting the upload form the IDE.
I seems that the program does not jump to the bootloader.
When I press the reset button the Pin13 LED stays off.
I reloaded the bootloader with my ISP with no errors but the problem stays the same.
(OS=Ubuntu 12.04, IDE 1.0.1)
Regards
Reinhard