The same here... I already got my second ICS update from HTC, but I still have the issue.
For me it is though a bit different as I don't have any problems after restart. I have the issue after I connected to a computer in "Disk Drive" mode. Sure.. the card is disconnected from the phone for this mode, it's OK.. but when it is reconnected after pulling the phone off the cable, my ringtones (which should be from the SD card) are set to system default...
Sometimes the ringtones disappear also from the list, sometimes they are there but still set to default one till I explicitely set it again to the custom one.
I did a workaround that I created a "Sound set" under "Personalize", next to "HTC Default", both having the same settings, and I switch between them when I have the issue, sometimes it helps, sometimes it does not have any effect either :-( the ringtones are still not those that the sound set shows.
Is it already registered as a bug?