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42 images?? You must be looking at a Multi-image window. I can't imagine opening that many images simultaneously.
Up until recently, I tried to process photos using a combination of Thumbs Plus, Nikon Capture, and PhotoShop CS all loaded at the same time. Worked well in the past, but lately I can't get much done that way. Could be because my files are suddenly much bigger (D2X RAW), but I don't want to go through a lot of testing to see what the real problem is right now.
And I've noticed that certain edits with NC seem to make NEF files undecipherable for Thumbs Plus. Don't know exactly what they are, but when the problem occurs the thumbnails can't be created by Thumbs Plus and it refuses to do anything with the files until I restart the application (TP, not NC).
This really is becoming a problem for me, because I really want to keep the NC controls in my workflow. I really hope Nikon and Cerious fix these issues soon...