They'll catch up eventually. There'll probably be a slight difference in temps, tho, especially if the other FW isn't exactly the same length and type as the probed piece. You'll just want to tweak things until you have desirable temps in both enclosures.

Hmm, are these two enclosures in a rack or separate individual cages? If they're on their own, try to get them at the same level height wise to keep the temps as close as possible.