#3 - Dec. 30, 2009, 6:01 p.m.
Q u o t e:
is this a known issue?
On the contrary, it's intended. I do apologize for any confusion this may have caused you, though. =/
During the Faction Change process, faction-specific quests—as well as faction neutral-quests which are part of chain gated by faction-specific quests (think Shadow Vault, Sons of Hodir, etc)—are removed from your character's completed quest log. Because of this, achievement
progress for "X quests completed" and "Complete X quests in Y zone" achievements may be greatly affected.
In your case, you've noticed that the quest counter for the achievement "3000 quests completed" is significantly lower after your Faction Change. This is normal, as most of your character's completed quests were wiped from its log upon faction changing.
You should still retain credit for quest-based achievements which were completed at the time of your Faction Change, though, correct? :)
(As a side note, I'd greatly recommend taking a peek at our Faction Change FAQ:
http://us.blizzard.com/support/article.xml?locale=en_US&articleId=28825)