good news! have read a bit about missing chunks problem.
Finally we decided that the lag and issues stemmed from these chunks, and shut down the server, and completley wiped the map and generated a new one.
Not everyones favorite idea, I know, but it worked perfectley fine.
And ill be honest, I think you might have to do this soon.
:DDD
We were on multiplaygameservers for our first host... not sure if that had anything to do with it, but stopping the server via the panel would just crash minecraft before saving. Stupid.
We switched to JestServers, an incredibly better host.
So my guess is that your server crashed mid save and caused these errors.
In the future, issue a /save-all command (or /#save-all) to save the map, then kick everyone (Use CommandHelper for cool alias creation like /kickall), then do /stop (or /#stop)
If you have a host with a control panel, shut your server down there AFTER you have done the above steps.
This will force save the map, then kick everyone to make sure no inventory loss (Possibly not a problem anymore), then stop the server "gradually"