weird battery charging

Hi guys
I have just had a weird thing with charging my trolling motor battery: the charger starts to charge for 5 seconds (yellow light) then says the battery is charged (green light) for 5 seconds then yellow light again for 5 seconds and green light for 5 seconds and so on.
I don't think my battery is charging at all...
I used it a week ago to jump start my car as battery was dead, I hope I did not kill it...It was full before I used it to start the car.
any idea on what the issue may be?

Your charger might be overheating and turning itself off, cooling a little, and then going back on. Is the charger big enough??

yes the charger is big enough, I have been charging the battery with it for the whole season last year. I don't think it was overheating as it did that as soon as I connected it to the battery. I stored the battery and charger in my basement which may be around 35-40 degrees F at this time of year, so maybe it was a bit cold instead. Do you think it could be the reason?
Also I heard a very low noise coming from the battery at the times the charger was showing "in charge" status for ~5 seconds at a time, something like bubbles popping to the surface when you pour some coke out of the bottle into a glass. But I never really paid attention to this earlier as I did not have any issue so maybe this is a normal noise and I am becoming paranoid I don't know...

Nothing wrong with being paranoid
A discharged battery will bubble a little while being charged.

I doubt if the cold has that big of an effect, but you could always move the battery to a warmer place and try that. If you have a good voltmeter, take a reading of the voltage right across the terminals without the charger on them.
12.7 is fully charged, 12.2 is only half charged, and you probably have a lower voltage than that.
Maybe you could borrow a charger???
Hard to figure it out from here...

I don't have a voltmeter but was planning to but one at some point so this could be the time to do it
The battery is a 120 amp hour marine deep cycle battery that was fully charged before I used it to start the car (honda CRV) using jump start cables, do you think that just using it to start the car could be enough to discharge it that much?

That is hard to say, but the voltmeter should tell the tale..

it is probably because the battery is cold and won't charge any higher. jumping a car didn't discharge it much. my batteries act the same as I have to keep them in the trunk of my car all winter.

thanks, I put the battery inside my appartment so it should warm up. will try to charge it tonight and see if it is better!

12.7 is fully charged, 12.2 is only half charged

Oh this is strange... how come it is not 12v as 100% of charge, 6v as 50% and 0v as empty? Is it because the output current always have to be at 12v or above for the electronics to work?

http://www.pbase.com/mainecruising/battery_state_of_charge

shows about what I said, you can google more detailed explanations

Ok so I tried to charge the battery after staying one day inside at warm temperature, still doing the same...
I just put an old car battery that was discharged and it seems to be charged already which is strange, unless this is a 24v battery and my charger minn kota MK105p) is not compatible with 24v batteries?

just bought a small multimeter at home depot today, and it reads 12.46 volts so around 75% charged. Should I let the charger on for a few hours to complete the charge? I am afraid to damage the battery if I charge for too long with this weird on and off cycle of charges every 5 seconds... what do you guys think?

when the charger cycles on and off it is in float mode or maintenance mode. it thinks the battery is already fully charged and it probably is close. it is not going to charge it any more. I have had batteries act this way when stored. once it has been discharged enough by use it will normal charge cycle.

Your charger is no good. I had one doing the same thing, It's in a land fill now.

It is only one year old so I hope I can have it fixed by Minn Kota for free... I will try to call them