Let's start with which version of ID you use. Is it patched to the latest update?
Do you start "fresh" with each new edition, use a template, or recycle the previous addition by using "save As" and deleting old content?
I'm using CS5.5 - and no, I haven't done any updating. Not really sure how to go about that!
I am using the 'save as' method.
Help > Updates... or download the latest patch from Adobe.com. CS5.5 is at version 7.5.3.
Recycling is not the best long term approach to making documents that update regularly. Godd as ID is, there is always the possibility of minor problems creeping into a file when you work, and they tend to accumulate over time until you have the straw that broke the camel's back.
Try exporting your file to .idml and resave as a new .indd and see if the TOC behaves any better (after you update to 7.5.3). See Remove minor corruption by exporting