Hi.  You really have three 6-volt wet cells? Not 2 or 4?

You can't have three 6V batteries on a 12V boat. Problem is not the charger if this is the case.. Also unless you know your Ah counter is both wired and programmed correctly it CAN NOT be trusted for SOC.

If your batts were taking 41A at 14.4V they were either not full or you are trying to charge an 18V bank. You may also have a shorted cell.. Start with specific gravity readings...

That's why I asked :-)

I would take them into BatteriesPlus or AutoZone (stores) and ask them to charge them and then load-test the batteries. 

Do you keep them topped off with distilled water?  If you've put in tap water or let it slide until the plates are showing a few times, then you may have trashed your batteries. 

I'm a little fuzzy on how to test a charger but perhaps others have advice? You can buy a cheap portable charger, as an alternate to your main charger and as a backup charger, and see if it is keeping them charged.  There are some recommended ones on Amazon.  Maine Sail probably also has recommendations.

Basically, you need to narrow down the problem.

Nigel Calder's book has an excellent section, containing just about everything you need to know about batteries and their maintenance.  I would buy that book and read it.  I had to read it a few times, before I understood it.
 

Britt
What Main sail recommended is really the best first step. Buy your self a $10.00 hydrometer Most Auto parts stores carry them. Below is the procure for checking your batteries. What your looking for is a difference between cells. One bad cell in anyone of your batteries could be causing this issue. 
There are many web sites that show how to use a hydrometer. Maybe even some you tubes.
 

Measuring Specific Gravity

Specific Gravity:

The most accurate and direct way to test the state of charge of a battery cell is to determine the specific gravity of the battery electrolyte. The higher the specific gravity of the electrolyte the higher the state of charge. The best way to truly monitor your system over it lifetime is to regularly take and record specific gravity readings.

Unfortunately hydrometers are not easy to use. Testing can be time consuming, there are possibilities for error and safety must be considered. For these reasons we present this bulletin.

Hydrometer Types

Hydrometers come in many sizes and shapes. We recommend a hydrometer with a float, contained in a glass vessel with a rubber bulb to draw the acid into the tube. Stay away from floating colored balls as the extra inaccuracy results in very subjective testing. The hydrometer should give you a numeric reading directly from the instrument. A good hydrometer is accurate to +/- 0.005 points so 1.265 could read from 1.260-1.270. The instrument accuracy should be known.

Method of Use

Exact procedures is instrument dependent and this is given as a general procedure and assumes a hydrometer with glass float and body.

1. Put on eye protection and rubber gloves.
2. It is recommended to disconnect the battery especially if on a high rate of charge / discharge.
3. Remove vent cap. Carefully insert the hydrometer into cell, not pushing down on the top of the plates.
4. Carefully draw liquid into the hydrometer and avoid "bumping" the hydrometer. Be careful the float is not flooded (too much liquid) or sticking to the sides of the glass tube.
5. Obtain a reading by looking directly at the float.
6. Repeat steps 3-5 to reconfirm reading.
7. RECORD the cell number and result.
8. If it is very warm or very cold correct the specific gravity for temperature. If the ambient temperature is fairly consistent and original gravities are taken when the batteries are put into service temperature correction is not as critical and only necessary if problems arise. Make sure electrolyte is not hot if just taken out of service. Let it reach room temperature.

An easy procedure is to number the cells starting with the positive cell and move from cell to cell towards the negative terminal. If this is part of a preventive maintenance program it is helpful to number the batteries.

Temperature Correction

SG of acid is temperature dependent. If the temperature is very cold or very hot this can lead to incorrect readings. To correct for temperature use the following equations the equations or below 70ºF subtract points (0.03 per 10ºF) and above 70ºF add points.

• Correction factor = (0.331 x Cell Temp ºF - 23) / 1000 or 0.003 pts per 10 ºF

• Correction factor = (0.595 x Cell Temp ºC – 12.5) / 1000

This is valid for 0-130ºF or -17.8- 54.4ºC

The following shows the approximate state of charge at various specific gravities at 77ºF / 25ºC.

 
ChargedSpecific Gravity
100%1.255-1.275
75%1.215-1.235
50%1.180-1.200
25%1.155-1.165
0%1.110-1.130

Hydrometers are at best accurate to +/-0.005 points. Voltage can be used to estimate state of charge, however caution must be taken when interpreting voltage readings.