You are letting Logic get up to speed, right? It takes two, three, maybe four bars to sync.
I have this problem, too, with my Lynx card. In OS X, Core Audio and Lynx introduce serious latency. My Logic audio buffer setting has to stay at 1024 samples if I wanna use Reaktor, and my on-board-the-card latency is 663 samples when recording at 48kHz.
Anyway, you can set your midi delay on each midi instrument in 'arrange' window. I usually have it set at +30 to sync best in my situation.
FWIW, I'm using a MOTU USB MicroLite with my Virus and Motif ES.
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G4 | Lynx L22 | Logic Pro | Virus C | Motif ES | ADAM S3A | Benchmark DAC-1 | etc.
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