IDE 1.01 will not complete upload after compile

Could use some help here,

I have definitely verified that IDE 1.01 is not starting my compiled program upload after the compile function is complete. I used IDE 022 to load the ASCII dump program and verified that it dumped using the Serial Monitor.I then opened IDE 1.01 and restarted COMM11 and attempted to load my comiled program again. After waiting 10 minutes and never getting an "Upload Complete" I shutdown IDE 1.01 and closed the COMM 11 port. I then restarted IDE 1.01 and found that the ASCII dump program was still in the processor memory by viewing the ASCII dump run in the Serial Terminal window. I think that this proves that IDE is not starting my compiled program upload for some reason. Any suggestions?
I am running Vista Home Premium and using a FTDI cable to communicate with my Arduino Mega 2560 which has no onboard USB to serial converter. I have independently compiled my program prior to selecting "Upload" so I know the progam will compile. For some reason IDE 1.01 is not starting the upload process. The fact that I can use IDE 022 to compile and upload the ASCII dump program should be proof that my FTDI cable and Arduino Mega 2560 are functional, but not with IDE 1.01.
Regards,
TCIII

What board are you using? The Arduino Mega 2560 does have an on-board USB-to-serial convertor. (Or did yours die somehow?)

You might try changing the stk500v2 protocol to "wiring" in the boards.txt file (in hardware/arduino in the Arduino software directory).