Problem using SD2 with multiple outputs - latency?

I was working on a drum track today and noticed some strange behaviour in SD2

I configure SD2 to have individual outs for kick, snare and hh and a stereo out for the rest of the kit.

I have a drum pattern playing in the step sequencer and have it looping, which works with no problems at all. However, when I start adding insert effects on the kick, snare and hi hat tracks, the timing of the individual elements is all over the place with regards to the other tracks in the song.

I've tried increasing overall latency, but it appears to make no difference. I suspect the problem is one of latency compensation in certain plugins, as if I freeze the tracks, then they loop fine. Rendering the unprocessed tracks to audio and then effecting them also seems to be fine.

Has anyone else experienced this behaviour, and if so, what do you do to resolve it? Do I have to tweak each plugin individually, or not use certain plugins. Also, is the delay compensation being introduced by SD2 itself and do I need diable it in SD2?

For information I tend use a combination of the following plugins (all free VSTs or included in Sonar X1b Essential) on my drum tracks:

Variety of Sound BootEQ MkII
Variety of Sound Nasty DLA Delay
Variety of Sound Nasty VCS Channel Strip
Per-track Sonitus EQ (for "surgical" stuff)
Alias Factor
FX2 Tape Sim
Studioverb (usually on snare only)