I have the same problem. I have a new Mega R3. I tried both Arduino 0022 and 1.0 on my Mac OSX 10.6.8. Sometime my sketch will upload fine, but most of the time it times out. Doing some Google searches, I found this seems to be a known problem, but I'm not sure how to fix it. I've seen some talk about avrdude, but I don't know anything about fixing, compiling and uploading a boot loader. Since this problem seems to be kind of old and my hardware and software are new, I'm surprised this problem still exists. What should I do?