It sounds like ThumbsPlus has trouble thumbnailing one or more files. As a result, the remaining thumbnails do not get made and a stuck task remains active in the background.
If you are using the program's default layout, you should be able to see that stuck task listed in the bottom-right "Task List" panel. It should say something like "Scanning XXX" where xxx is the name of the folder in question.
If so, what you could do next is go to that folder and set the sorting order to None (the two rightmost pulldown boxes in the bar just above the thumbnail listing set the sort order - set both to 'none'). Then, the first file in that list that shows as a red cross on a white background (i.e. the first non-thumbnailed file) is likely to be the culprit. This file might be corrupt or ThumbsPlus cannot thumbnail it for some other reason. You could (temporarily) move that file elsewhere and re-launch TP to see if that solves the problem.