Ok one at a time:
Is there an auto-reject trigger that activates if a user flags too many comments at once?
I hope not except for some spammer, but still I hope not.
Did I get on the bad side of some moderator?
Maybe... maybe not.. maybe you rock and are awesome. All serious here, as a moderator we really do not have time to get to a point where we are angry or have a problem at somebody. Between real life stuff, Q/A in this site and the amount of mod activity, one would be lucky to get to know at least 10 users.
Did I do something wrong?
For what I could see no. You have not done anything wrong...yet ^^
What is going on?
Maybe a mod though the opposite or had a mistake. Mods are not robots..yet ^^
If you want (Maybe you already did) when flagging a comment you could add why it should be removed/edited/moved... That way it helps to sort the problem out, from many flags we get everyday. Well at least in my case (And I am the slowest of all moderators, so you can imagine the rest).