cueblast,
I tried to reproduce this setup and I ended up with the same issues. In my case, Omni 1, 2 & 3 played back instantly. Omni 4 & 5 - as mentioned - with a huge "mididelay", let's say 1minute after stopping the sequencer...
It's such a great piece of software but there are still A LOT of issues which make it quiet unreliable.
Mac Pro 2 x 2,93 GHz - 16GB RAM
OS 10.6.1
Logic 9.0.1