Whats the deal with file references.

I have this large assembly which I like to work on today. I did a check-out on the assembly and it just sits there updating file references.

When I cancel it says my assembly is checked out.

When I open it in solidworks the first time it doesn't open and the second time it says its read-only.

We did a reboot to the EPDM server and its still acting flaky.

Suggestions?