Could be the board you are using in the configuration you described. I tried the same thing on my suspended wood floors which are carpeted. Vibrapods on the carpeted floor, MDF board on top of them, then the spiked speakers on top of them. Sounded OK but not ideal. When I substituted a 1" thick maple wood chopping block for the MDF the transformation was amazing: fast, clear, dynamic, musical and I've kept them that way since with a high degree of satisfaction; 2" would probably be even bettter. I got the chopping blocks from TJ Maxx for $10 apiece but you can also get them at Bed Bath 'N Beyond, Ross or a hardwood supplier for reasonable cost. If you can't find maple try other hardwoods. I've got bamboo cutting boards under my spiked monitors on stands and they, too, sound significantly better than the MDF or directly onto the metal stands.
Also, make certain you have the correct Vibrapods for the weight they are supporting.
Hope this helps.