Indoor Bike using FR955 with Tacx Trainer

Using my FR955 directly with the Tacx trainer I noticed at some points that the effort required to move the chainring is not consistent with what it is requesting for and in the gear I'm in it is not constant.

For example: an interval requires 250W, for 18 minutes, I put the big chainring, 3 pinion, it starts well but then the resistance becomes very large in the same interval, something that does not seem consistent to me. Then comes the Rest stage, I want to do another 250W interval but I can no longer use the same ratio of chainring/pinion because the resistance is different, and it is not logical, since they are the same 250W.

Anybody experienced similar problems?
Is it a drawback of using the clock directly as it runs slow or desynchronized from trainer or doesn't keep the Workout constant with the power requirement?
I'm going to try the next Workout directly from the computer, but wanted to see if anyone else has had it happen.

Thanks!