I just built a test project to test if this occurs on my system. My answer was - no - latency compensation works fine here using OSX 10.6.4, Logic 9.1.1, VEP 4.0.6150. Everything was running at 48kHz as it always is here.
I wasn't however using Omnisphere or tempo sync. My test was simply to create 2 instances of Kontakt 4.1.1 and to load a short clicky drum sample. One of these instances was hosted locally, directly into the master Logic project, the other instance was loaded via VEP into the 64bit server on a slave Mac Pro.
I found that the clicky drum sample was properly synchronised between the local and remote (VEP) instances of Kontakt 4.1.1 during playback and for both online & offline bouncing.
I guess your problem is either specific to your system, or to Omnisphere.
I can send you my Logic project file & metaframe if you would like to test it.