At this point I've now tried arduino 0021+4.5.3, 0022+4.5.3, 1.0-beta1+4.5.3, all of which are broken for mega2560. Meaning, compiles and flashes fine but doesn't run assumingly because of the register save/load bugs. I then tried 0021, 0022 (again), and 1.0-beta1 + 4.6.1, all of which are broken for mega2560, typically unable to even compile.
This is especially frustrating as I can find projects which reportedly are using mega2560s + avr-gcc. The ArduoPilot seems to be one such project; though perhaps with a 1280 (IIRC) bias. And it seems winavr claims to support mega2560. So I guess the real question is, what combination is working? Which, if any patches are being applied? And in which combination is it being used with the arduino core libraries? Even stranger yet, why are linux distributions providing a known buggy compiler which has been known to be broken for over a year now? Fedora seems to be stepping in the right direction but I have no idea if they have actually found success.
Thus far, I can't stress enough no one should be using mega2560 until this this silliness becomes a priority and gets resolved. As you've pointed out, this nonsense has been going on for over a year now. Why it is this painful to simply get something to cleanly compile and reliability run with the mega2560?
It seems you're using arduino 0021. Which compiler/platform are you using? Are you using winavr? Based on various readings, I get the impression winavr is 4.5.x + a bunch of patches. So perhaps this is why the majority (assuming they are using winavr) are finding success with the mega2560 series?
Is this the right place to post this type thing?