Ouch. o_O Fortunately, those objects (or solutions involving the nuke, which I'd be very surprised if it wasn't also affected to some extent) are quite rare, and it's primarily my own levels that use the former.
I don't think I've ever modified the code that handles the actual counting down, so this also raises a question of whether Lemmix may have an inconsistency from DOS in this area too, at least with the countdown (obviously radiation is irrelevant there, but it has timed bombers).
In regards to replay breaking - it's annoying, but should not be the primary factor in making a decision. The correct approach here would be "make the countdown start at 9 and work properly (17 frames per 1 second)", not "leave it as is" or "do weird stuff in order to preserve replays".