Is this something that just started happening (after some time functioning correctly), or is this an all-new install?
What is the length of your wire run, wire gage, etc? What kind of trolling motor plug (if any) are you using? You sure all your connections are good and clean?
(Trying to get an idea of your voltage drop, good connections, etc.)
What kind of charger you got? Is it a smart charger that gives an indication of battery condition / charge? What kind of batteries? You say the batteries are new, any chance one (or both) of them are bad right from the store? (it happens!) Maybe go get those load-tested. Got a multimeter?
(Could be just a bad battery)
Do you happen to have two other known good car/boat batteries and a couple sets of jumper cables or such you could use to rule out a problem inside the TM's electronics / internals?
(I'm wanting to get one of these GPS anchor TM's myself, but I'm starting to get scared regarding their reliability!)