The quests are written against the PEQ database as PEQ handles both. The format issues occur because so many people write quests for PEQ, and many of thw quests were written years ago before any guidelines existed. There are guidelines now on the PEQ forums for quest team members, and for the most part most stick to the syntax fine. That's the important part, as that ensures everything is uniform and works fine.
If you find bugs with quests or database, it's best to report them here:
http://www.projecteq.net/phpBB2