Depending on where your probe is it can vary, but your setting on your thermostat will never be the exact floor temp in the tubs. The important thing is that your thermostat keeps it steady at one temp while your tubs stay steady at its temp. That said 100/90 is a pretty big difference. My first guess would be that the 3" tape is having to work harder cause it is so thin. I have no idea why rack builders are using such small tape! I prefer thicker tape working less hard and providing a bigger even hot side. I would use 6" tape in your setup, which is why I build my own racks. My floor temps are 80cool-90hot with ambient temp at 83-85ish and humidity at 55-65%.

So I think you are fine as long as your reading your hot side floor temps correctly without any substrate over it.