I'm working with a Mega2650 and IDE 1.6.9 and have successfully uploaded a sketch to it many times, but for some reason now there are strange problems. It appears to be uploading a previous version of the sketch and not the version that is shown in the IDE on the screen! I can upload other sketches and they run fine but when I upload the problem sketch that I have previously modified and uploaded many times, it does not upload the version I have open in the IDE. It also has intermittent trouble uploading this sketch and gives an error that I didn't capture yet. The only thing I can think of is I think I accidentally selected "Fix encoding and re-load" on the Tools menu once by accident when I meant to open the serial monitor.
Enable verbose upload + compile, and try to capture the error and post it. In any event, logs from a successful attempt where you don't think the code has updated would be of value.
If it says the upload completed successfully, it has read back the code and verified that what's on the chip matches the compiler output. So you have either wound up in a very mysterious issue where it's using a stale binary, or - much more likely - the thing you're changing in your sketch doesn't have the impact on it's operation that you think it does (this is what it usually is when someone complains that it's uploading the previous version of a sketch).
Thanks for your suggestions, I'm not sure what changed, but it uploads now and I see the changes as normal. I Since then I have restarted the PC 2 times, and ran the update boards option. This was very strange to see. I am running Win10 64bit professional on a Dell Optiplex 580 w/ 8GB ram. I am uploading to the mega through a 5 ft usb extension cable but normally don't have issues... I think.