Today on IRC Kliment was kind enough to help me figure out something that has bugged me for quite some time now.
Whenever I pause a print in pronterface, jog the z axis, and then resume the print it slows down to a crawl. Kliment explained to me that the z jog sends its own f command, which is a speed setting for the next move. The z axis moves much slower than any other axis, so that when I return to the unpaused print, all of the axis are moving at the (slow) z speed.
Even if my explanation of the problem doesn’t make much sense, the fix is easy. Just jog x or y before you unpause the print. I usually jog .1mm right and then left and then hit resume. Now it starts right up again at the correct speed!