Sounds like you're saving as GDBM and it's hitting the file size limit. Same problem I'm having. IE, Maemo Mapper won't save as or use existing SQlite3 databases. Only legacy GDBM. I'm still working up a fix for that.

EDIT: Ok, I've got part of the problem solved. Apparently MM downloads some kind of list of repositories and it in turn has a hard coded reference to using GDBM with Google Street, and several others. Open Street, oddly enough, correctly uses the sqlite format. To fix this you have to add a new map repository, select sqlite for its format, and then add the url for whatever map repository you want to use. After that it does correctly generate a proper sqlite3 database. heh.