Import does not run audio analysis. They are different.
Do you have any MP3 or APE files you could test? This isn't a problem I'm familiar with. I'm wondering if it's FLAC specific.
I experienced this problem a lot with both FLAC and mp3's in MC13 not to long ago, so it's not limited to FLAC. However, this problem is a bit strange because it appears to exclusively happen when using the right-click->analyze.. function that opens the queue window. Why I think this? Because when I initially tried importing my library of 20000+ tracks, all the files had replaygain tags and this meant that none of them were automatically analyzed on import. I then tried working trough the files scanning batches of various sizes at a time (everything from just a couple of files up to a few thousand), and it would always eventually crash. Sometimes it crashed when only analyzing a few files, sometimes it would keep working for hundreds of files, once even ~2000 tracks before crashing. When it happened, I'd start MC13 again and try scanning the same files again and no problems were encountered with them...but of course, it would eventually crash again with some other files (so it appears to have nothing to do with the files themselves). I tried rewriting the tags with another player, disabled DEP, removed my antivirus/antispyware programs, updated audio/video/chipset drivers, scanned the HDD for errors, defragmented both the system drive and the one holding my music, tried in both XP and Vista...all with the same result.
Frustrated, I fired up mp3tag and removed the RG track gain from all of the files (so that the auto-analyze function would get to work), cleared my MC13 library and let it import everything again. This time, many hours later, all supported files (mp3/flac) had been analyzed, had updated tags with BPM/RG++ and not a single crash was encountered during this process.