I hope it isn't too late for the dev team to fix this, as it has been a long time since any other bug reports, and this is a REALLY bad bug.
Anyways, if the Time Control setting isn't changed back to 100% before you leave a level, the game will remain running at whatever time speed was last specified. The Time Control can affect the Title Screen and any other levels opened up without already exiting the whole game. This bug even goes into the Story Mode.