I can't really say much about the Unhandled Exception errors (I'm the database admin and not a programmer): I do get them also on Windows (when running crc32 checks). Normally it seems to happen when I'm trying to check a large file in an old game list after the updated database is loaded in. I've taken the same problem rom, created a new game list for it and it verifies with no problem. What I'd suggest is to use the Rominator feedback button to get in contact with hankchill.
And yes, people seem to make up number lists. Previously, Rominator follows GBATemps' numbering scheme, but then along came the DSi enhanced games: Some sites branch off around there (example: GBAtemp splits them off as DSI0001, et al), some sites include them in their regular numbering, and (IMHO) some sites are just plain nuts.
When I asked hankchill (originally) which way to go, he told me to use best judgment so I did. Problem with GBA's method is there are actually DSi exclusive games (which personally, I'd number DSI0001 through whatever). Then again, in my view, pretty much everyone's system is wrong: Before the DSi was officially released, about 15 games surfaced that have never made it to a list. The trick was to go with what works for you.
For personal use, I do try to use Advanscene's list as well as Rominator, but their numbering is also slightly off (7 roms with different numbers the last I checked).