My onboard chargers red charge light will turn off and on for no apparent reason (it is supposed to be on all the time when plugged in) and hasn’t charged the batteries enough to get the green charged light to turn on in a week. The charger and batteries are only 2 years old also. Anyone else ever have this problem or have any ideas on the problem? 
Did you check the fuses? I had the same problem and one of the inline fuses had blown.
What brand of charger is it?
Checked the fuses after your suggestion and they were fine. Hadn’t checked them before. Just assumed it wouldn’t work at all if one was blown.
It is a Guest 8 AMP Charger.
I also can’t find the manual, so if anyone has the same charger and it says anything in the manual about this issue I would appreciate any help.
almost sounds like a bad connection.
Have you tried cleaning up the terminals and wires and reconnecting???? 
Even a regular battery charger will act up if not getting a good connection.
When was the last time you checked the water levels? I have to add to mine twice a year…
On my charger if the charge level in the battery drops too low the on board will not charge it. Try charging your battery’s first with a regular charger and the plug in the on board and see what the lights do. Also as said before check the water level.Good Luck!!!
Thanks for posting the manual BrianK.
For the problem I was having it said I need to call customer service. They informed me that the charger was to small for the batteries and system it was being used on and that it was probably shot. Interestingly I bought the boat brand new and the charger and batteries were included. The guy at customer service said this happens quite a bit. 
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