According to the PA site, Howard had written to the PA boys asking (demanding?) them to crack down on PA forum-goers who were using AMD characters as avatars. Included in this letter was the statement that Howard had already "shut down six web comics that were using his art", thus potentially implying that the same could happen to the PA site, if this alleged copyright infringement was not dealt with quickly.
Ironically, Mike "Gabe" Krahulik's mention of the letter and incident on the PA site, complete with a link to Howard's webcomic, inadvertantly temporarily caused a shutdown of Howard's site due to a CPU-usage, traffic overload.
While complete details from both sides are yet to be made available, Krahulik brought up some very salient points on Copyright and Fair Use. Meanwhile, Howard has not commented on the issue on his own site, which has just recently come back online — with the exception of saying that "Penny Arcade's recent linking to this site has 'wanged' us."
[UPDATE DEC. 12 (11:26pm): Howard posted a response of sorts to the whole incident on his site today. Essentially, the response consists of a copy of a letter sent to someone else, where he tries to explain his side of the story. An interesting coincidence(?) to take note of, as well — as of this writing, the PA site appears to be down, and has been down for at least one hour.]