Road Fan

Several things could be going on, not all of them in the trainer. If your hub bearings are getting hot due to pressure or perhaps are adjusted too tight, I could see increased resistance when you are pushing harder (pressure in the bearing systems of your bike) or dirt in the bearings causing similar resistance to rolling.

So If you have the mechanical chops to tear down your fluid trainer, I think you have the chops to give your bike an overhaul, clean, regrease, renew bearings as may be necessary, and readjust the bearings so as not to have excessive bearing pressure. I tend not to use preload in my bearings, I would suggest giving that a try. But you still should not have any play in the bearings.

It's still of value to finish overhauling your trainer, but don't neglect renewing the hub, BB and perhaps freehub bearings.

The theory here is, with all known good main bearings, there should be zero change in rolling resistance with pressure, speed, heat buildup, or running time. But I could imagine standard BBs causing such trouble if they are not up to snuff such as dirty, grease not fresh, worn, or too tight.