High rpms raise your HR without increasing your power or speed. Don't worry about it. Buy a set of resistance rollers and get rid of the trainer. Alternatively, increase the resistance on your trainer so your legs hurt pretty good after an hour at 90 cadence. Gradually over a couple of months, try to increase your time at that power to 2 hours.

Another kind of "fun" thing to do is to use a low resistance on the trainer and take your cadence up to 130 or so or to where you start to bounce on the saddle - and hold it until your legs can't take it anymore. Try to get that high cadence time up to 40' without a break. Your high cadence HR will gradually come down as you get more efficient. See, there's lots of fun to be had on a trainer, even if the cranks aren't the right length!

Basically, I wouldn't worry about it. My wife rides 149 cranks on our tandem and 165s on her trainer. It's not an issue of adaptation, just an issue of working hard on either machine. If your legs don't hurt, you're doing it wrong, that's my motto.