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).