Tony: if it were improper pairings, that wouldn't explain why it stopped working when it once was.
It would explain it if there was an unexpected addition of new RF interference somewhere nearby. Hypothetical example: The air conditioning in the building starts getting used in the spring, and this is causing new electrical noise that wasn't there until recently.
If I'm understanding your problem description correctly, you're not seeing an obvious malfunction, rather, you're seeing an unexpected performance drop. Right? Bad wiring can do that at unpredictable times.
I just tried setting my NIC to full duplex manually, and it worked just fine.
If you force your NIC to half duplex, does the performance drop to match what the other downstream computers are experiencing?