What is the vibration frequency of the vertical motion on the I-beam skid? Does it make the speed of the pump shown or something else that shares the skid? Is there a lot of pipe motion as well? Did you inspect all pipe supports and hangers? A 2-step approach could be considered:
1) Epoxy grout under I-beams (possibly raising about 1/2" or more to get suitable grout thickness along with epoxy-set anchor bolts.
2) Cement non-shrink or epoxy (preferred) grout to fill entire I-beam skid frame.
A little more detective work might lead to a solution that is both effective and has lowest cost.