I haven't really noticed any more tension between them two then any other person Artie gets irritated with. Its true that he has been more testy with Gary since the Afghan trip, but maybe Gary has "allowed" Artie to push him around so it just comes sub conscientiously. I don't know if you understand what I mean, but it's almost human nature to increasingly get annoyed/agitated with someone the more and more they don't respond to it.
Gary's just pissed because he was defending Artie and it made him look stupid when the lies were exposed. Not that he needs any help in this regard - my favorite parts of the show are when Howard does the Gary voice and Fred starts playing the bababooey songs back to back.