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I haven't modeled plenums in OS yet, but I've had plenty of of experience troubleshooting geometry errors. First, if you aren't using the most recent stable release (currently 1.4.0) I would suggest updating your model. Second, you've already mentioned it, but I will echo the need to be very careful when creating OS geometry in the SketchUp Plugin. Make sure you entirely delete any mistakes and if you're adjusting spaces/zones make sure your lines recognize adjacent ones otherwise you might be left with surfaces that don't recognize each other - i.e. do not have complimentary outside boundary conditions. In general, I use the following workflow:

1. Create geometry in SU, intersect surfaces, match surfaces, and visually check outside boundary conditions
2. Create thermal zones either manually in SU, using the SU user script, or manually in OS
3. Move to OS and run without HVAC by setting ideal air loads on to test the geometry. This can be done manually for all zones or by writing a measure to do it if your model has a lot of zones (happy to share mine if you need).
4. Use the measure "Add Output Diagnostics" with "DisplayAllWarnings" selected - this will give additional details in the ERR file to troubleshoot any severe errors.
5. If there are geometry-related errrors, you can use the "Search Surfaces" feature in SU to find those mentioned in the ERR file and fix.
6. In extreme cases, I may manually delete OS objects from the OSM file, but this should be avoided because it can cause additional errors.

...hope that helps.