First off what switch are you using? What features/config? what else is going on? I don't quite understand your setup here, but I'll try based on what it sounds like.
It sounds like you are dual homing PCs onto different networks. what are the internal routing tables of the PCs? what about the metrics? how about the router config? it could be local routes with the same metric and one works while the other has a misconfiguration. that would cause intermittent issues.
If you are to rule out network causes of intermittent issues, I'd look for things like rate limiting or other COS mis-configurations.