Sounds similar to a problem I had with one of my graphics cards. For no apparent reason it would fail and then restart (I'm using windows 7, and I'd get a message pop up saying "your graphics card has recovered from a fault", or something like that). The graphics card would restart okay, but GUIminer would sit there doing nothing until I stopped and restarted the mining operation.
So I did a little digging into the event manager on Windows 7 and found that every time it did this it would generate a fault code in the "system" log. Event code 4101 I think it was.
Now.. Windows 7 allows you to assign tasks to specific events. So I simply wrote a batch file to stop and restart my GUIminer program whenever this event occurred. Problem solved. Here's the batch file I used.
@echo off
taskkill /f /t -im guiminer.exe
taskkill /f /t -im poclbm.exe
ping 1.1.1.1 -n 1 -w 30000 >nul
start C:\Users\admin\Desktop\guiminer\guiminer.exe
exit
I don't know what operating system you're using, but perhaps you can use a similar method to stop and restart your instance of GUIminer.