I'm surprised it is happening... but I'm not a Cubase user so can't offer any specific advice.
You could try inserting the same compressor plug-in (but set to 1:1 with the threshold turned up as high as it goes) to provide the same processing delay (but without adding any compression) in the clean drum group. That might resolve the problem....
However, the fact that it happens without a plug-in inserted in the FX channel implies something odd is happening to delay the pre-fade send in some way.
Are you sure nothing else has been routed inadvertantly to either of your drum groups, or FX channel -- or something is going to one of them AND to the main output? Easily done and could cause the effect you're describing.
Technical Editor, Sound On Sound