Make sure you don't have problem with fiber itself. If possible, rent fiber tester (we use Microtest LAN Tester with Multimode Fiber Adapter), to get readings on your link. What these testers do - they check your fiber according to production specifications. Do same readings several times a day, because we had bad fiber which gives us bad reading at certain time. Later we discovered that we had some "open" fiber exposed on sun. If you can't find where to rent this tool, may be hire someone to make these testings.
Another thing to consider - if you have more than one link between locations. In this case errors on interface may cause Spanning Tree or routing recalculations, which may cause delay in traffic.
Not sure about 3Com switches(I have Cisco), but try to turn on all logging, probably debugging, may be forward it somewhere with Syslog, and watch, what's happening during this "blackout" moments.
Good luck.