Few questions pop to mind first.
What version are you using? It could help us diagnose the problem
Are you using Lightweight mode? I've seen similar behavior in lightweight mode.
Did you do a SolidWorks RX to see if it found anything? Perhaps your graphic card is not supported?
Does it only do this on a particular assembly? If so, what about if you make a new one the same way, does it behave the same?
I fixed the mates that where flagged as errors, did a check in and closed. When I reopen all was finally in order but only when reopened, simply fixing the mates was not enough.
Glad to know everything's back to normal.
Assuming that the graphics card and driver are certified for use with SOLIDWORKS, there is one method to correct odd graphical behavior in part or assembly files...
1. Open the file
2. Press the spacebar key
3. In the 'Orientation' window, click on 'Isometric'
4. Press Ctrl+Q on the keyboard
5. Save, close, and reopen the file