:-/ same pb happened to me.
Every thing worked perfect while using arduino-007 and then arduino-010. Then I made a real big mistake while testing a prototype interface (I fed the +5V with some +12V high amps
). So as to say, I prepared a roasted ATMEGA168 :-[ . I checked it anyway: power supply is OK, FTDI interface is OK, but communication problem with the processor.
Here is the important information: I decided to upload a fresh bootloader, so that I added to install WinAVR on my PC. Since that time, I cannot launch arduino.exe, unless I use the run.bat script. (And my processor is definetly dead)
Very confusing indeed :-?