You can try the 'Real fix' as described in this article. http://kb.mozillazine.org/Compacting_folders#Real_fix

Thanks for the tip. I have now applied the "real fix" and will see how T-bird behaves.

Regretably, starting with a fresh inbox and using "repair" hasn't solved the problem. I'm still getting mismatched headers and bodies and losing some bodies. Losing bodies is not a satisfactory result, as sometimes I need to know whether I've received a certain email or not. With the present performance, I can't know this.

look at stopping anti virus scanning of the Thunderbird profile folders. most issues with mismatches relates to index files and stores getting out of sync. A principle cause is anti virus locking one or the other files to scan it just when it is being updated. Another is streaming backups such as time machine that start backing up the modified file about the same time as the next lot of mail is due to be added.