Well I tested all connections using my Fluke cable tester after I ran the wiring and didn't find any problems. I suppose I can check it again. But then again, if I did in fact have a miswire or faulty jack, I wouldn't be receiving network connectivity to those machines, correct?
Just to clarify - you could have miswired and faulty jacks and still have connectivity - the tcp/ip protocol suites are surprisingly tolerant and will more often that not handle network errors transparently (as they are designed to do), and frequently these errors can only be observed as you have done, as a drop in throughput rather than an outright failure.
A few more questions come to mind ...
What Fluke tester were you using and what does it check for?
Are we talking cable certification or cable testing?
What type of cable did you run for your gigabit links?
Last, but by no means least - are you sure that TrendNet router supports jumbo frame? I had a quick look at the data sheet and there is no mention of jumbo frame.