I bought a new Minn Kota Endura Max 55lb thrust transom mount motor for my 12' aluminum boat, which I have always powered with only a trolling motor since I fish mostly small lakes. Anyways all of the sudden my motor stopped working at all, especially in reverse. If I would let it sit for a few minutes and disconnect ot from the battery, it woild work again, but eventually it would fail to engage when I put it in reverse. It would often not work in forward either. I am sending it back to Minn Kota since I just got it and its stilln under warranty. Anybody have any ideas what the problem is?

It is messed up send it back and get a new one.  I've had pretty decent luck with Minn Kota warranty issues.   I had an issue with a relatively new Minn Kota (2 years old or so) that stopped working.    All I was out was time & gas (I had to drive it to Springfield, MO, to the warranty shop.   I had the day off and it was easier to drive to Springfield & back than it was to mess with shipping it.   Also the warranty shop was right next door to the original BPS, so I had to get some stuff and look around while I was down there.

Anyway - 3 weeks later when I again had to pass through Springfield en route to a BFL  tournament in Kimberling City, they had the trolling motor ready for me.  They even let me pick it up on my way home and now while I was going to the tournament.   That motor still works.

Most of the local Minn Kota service centers can take care of this for you - is there one nearby?

http://www.minnkotamotors.com/Authorized-Service-Providers/

...not all of them show up on the site, you might want to call around...I'd try Cabela's.

Sent it in, they have it now. I hope they replace it rather than try to repair it. At least it's going to be a week or so of unsettled weather and a bunch of cold fronts during my down time.