This is an easy fix. Well should be. Disconnect the wires at battery #2. Now install 2 jumpers from battery #2 to battery #1 (neg to neg and pos to pos). http://www.crappie.com/gr8vb3/showthread.php?t=48674 Look at the first picture, bottom diagram (12v in parallel). this is what you want to wind up with.
Now go fishin. With the 2 batteries in parallel you will have twice the run time.
With the old 12/24 system when you flipped to switch to 24V it connected the 2nd battery to the TM. Now when you flip it, that 12V has no place to go and you are still running on just battery #1. So you wind up with a perfectly good battery sitting there never being used. Since you have to disconnect the batteries to make that change it wouldn't hurt to have them load tested to be sure they are in good shape. Hope I made sense.