My answer would lie in whether you're putting out the same amount of power, but at a lower hr. That would mean you're getting fitter or more efficient.
If you're putting out less power along with the lower hr, I'd consider why. For me, it usually just means I'm sick of the trainer. But, you could be overtrained. How's your hr outside, when compared to usual? My hr is much easier to raise outdoors. Motivation makes a difference.
Another thing to consider: have you changed your gearing during for the intervals? My experience has been that after doing intervals for a while, and getting better at them, my freely-chosen cadence has actually dropped (even as my power output has increased). Typically, people find that producing the same power with a lower cadence leads to a decreased hr, but more muscular fatigue. As you get better at the intervals, you should become more able to tolerate localized fatigue. Hence, a bigger gear may feel fine, but the hr response may not be there. This is what I've experienced lately.
So, if you have dropped your cadence a bit, making sure your cadence is consistent (i.e. using a smaller gear for the same power output) might help you get your hr where you want it.
Personally, I'm just going to do whatever keeps improving my power at threshold.
Last edited by tadawdy; 02-21-10 at 12:54 AM.