draythomp:
I've had this problem a number of times. With some luck it is possible to recover by holding the reset switch until the upload starts and then releasing it. This will take several tries to get right. However, the most reliable way is to replace the bootloader. I fought this problem for a solid year before I talked someone into fixing it and providing a bootloader that works.Take a look at my blog page on the final resolution to this problem at: Desert Home: Arduino Mega2560 - Wrapping up the Bootloader Problem
Funny, the folks at Arduino said they would make this part of the distribution quite some time ago.
I followed your frustration working with the arduino developers and it's still amazing that the current arduino IDE distribution has not updated the mega bootloaders even after all this time.
Also do you know of an updated mega bootloader available for the mega1280 board, that fixes the same two problems?
Lefty