When I plug in my charger I have flashing red and green lights. Any ideas?

It usually means you have batteries that are to low for the charger to charge them. Try putting one of the old standby chargers on each battery until they are coming up in charge then put the on board charger back on them and see what happens.
I don't know much about the Stealth but the book should tell you what those flashing lights represents.

are you sure you have them hooked up correctly?

It may mean a battery is too low or perhaps the cell is bad in it. It is always a good idea periodically to charge the batteries individually to full capacity. Those chargers are in my opinion the best made. But, if one battery is low it will not charge it to 100%, it may charge the other 2 to 100 . Over time that one battery may only be charged to 50% causing the others to be taking more of a strain than needed. I usually charge mine the old fashion way once a month to keep them equalized. I have never ran my trolling motor down with that charger. This is my second boat to have one. I once fished 3 days, 1 practice day and 2 tournament days and never was able to recharge at the campsite and was just fine.

Thanks for the help!