Fair points about Thunderbird. The main benefit of Mail.app is that it integrates nicely with Spotlight, making it easy to search your own mail. Also, Thunderbird's use of Berkeley mbox means things can get slow and behave strange as the box size gets into the gigabytes.

At any rate, the problem turned out to be that Mail.app's importer fails to understand deleted messages (which are still in the file, but marked deleted). Asking Thunderbird to clean-up the files seemed to fix the problem and everything is now properly imported.