This happens if you touched your MXD.
So for example when you create your MXD and make it a ArcGIS Service. Sure you can use the MXD again to play with and such, maybe modify things, but never save your MXD again. That's my rule of thumb. Any changes to the original MXD will cause a checksum error.
So instead, of using the original MXD, I make a new map document and bring in the featureclasses that we are using and then perform analysis and maps and such, and you can save that mxd no problem.
Leave the original mxd alone.
I suppose you can open the original MXD and change things back to what it was when your synchronization worked. I hope this helps.