First of all, I have a 2005 Ford F150 FX4, and tow a 2001 Mastercraft X-Star.
The other week, after I had towed my boat out of the water, I put the boat away where I am normally store it. Shortly afterwards, the truck started vibrating quite a bit. I stopped the truck a couple of times, eventually putting the truck from 2WD into 4WD, and it stopped. I'm not sure if this was a coincidence or not. Anyways, I then put the truck back into 2WD and it seemed ok. The weekend was over at this point and I went home... no problems afterwards. Last weekend, I came up and put a smaller boat in the water (2400lbs Four Winns). I noticed that at the end of the weekend, as soon as I left for home, the truck started shaking again. Again, I stopped the truck a couple of times, messed with engaging and dis-engaging 2WD and 4WD. THe problem stopped eventualy. I went home, I took it to Mister Transmission and they couldn't find anything wrong. Anyways, no problems all week. Fast-forward to today. I was towing the boat and the truck start vibrating while I was actually towing this time. I stopped the truck, I didn't bother with the 2WD and 4WD this time. I simply geared down to 2nd gear (this is an automatic, not manual truck), and the problem didn't come back. I put it back into Drive from 2nd gear eventually, and the problem still didn't come back. I have driven about 100kms after that incident today... no problems!
Anyone had anything similiar to this? I'm not sure if it's transmission, it sounds like it to me but I may be barking up the wrong tree. I'm not a mechanic by any means. The problem definitely seems to surface during and after towing however.