World not saving? And Connection Reset spam!

So after doing some plugin testing with the 1.3 RB, I finally decided to upgrade my server. We have a fairly large player base, so I wanted this to go smoothly. After updating, the server started perfectly with no errors, and everything seemed fine. But then I have noticed 2 big issues.

First issue, might be minor, but in console I am getting "Connection reset" every 3-4 seconds. Not sure why that is, but my test server wasn't getting it.

Second issue, it seems anything my players build is not saving. Example, I build a dirt house and then /spawn and leave that area for a couple minutes, come back and anything I did there is now gone. Pretty major issue, and not sure what's causing it. I am going to test removing my MineBackup plugin and see if that helps. Otherwise, is this a known issue with 1.3? I thought it was fixed with Dev builds...

Hope anyone can help, thanks!