"This topic will automatically close in 3 months."

@Jody,

On the assumption (quite possibly premature) that you have done this, it appears not to have been applied to topics which the previous “Close 3 Months After Initial Post” has been applied. Had it been, then this topic would be showing that it will close in 3 months (since the last activity is today) instead of the 1 month that it is showing.

IMHO, the correct action - if possible is to change all topics that have the old (since topic creation) criteria to the new (since last activity).