I've the same problem but inside Autocad 2010, I'm using annotative dimensions and 3D clip, and no matter if I use text annotative or not I'm getting the same result, I can't see the dimension lines clips but in all layouts I see always dimension text isolated
What type of entities are you using? CAD polyline, line, etc; FDO data?
A quick thought may be to query by elevation each level to a separate dwg so only lines from one level and associated data show in the map.
if you have FDO data you may be able to theme and do away with labels.
Possibly you can provide some information and possibly a snippet for other to look at how you have organized your map?
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