The OP says in the end, after trying various isolation methods and spikes, he found it sounded best if the speakers were simply placed on the floor. Hard to say why but I suspect what's happening with a suspended speaker is complicated by various factors that may sometimes lead to worse results. I'm speculating about what might be going on. If the floor is resonating at certain frequencies due to airborne sound stimulation, which I would bet is causing far more audible effects than solid mechanical transmission in the majority of cases, that will be changed somewhat by putting heavy things like speakers, equipment racks, and furniture on the floor. And if those things are suspended in various ways that will have further effects. It may just end up shifting the primary resonance to different frequencies and different parts of the floor, which would explain why it sometimes sounds better and other times doesn't.
Or it could just be that some like this added distortion. It is not unususal.