Tom, You may have the WFCO Converter wired wrong (based on what you have said above). The WFCO installation instructions are very confusing and border on non-existent. The WFCO Converter/Charger is just that. It functions as a converter (converting 120VAC to 12VDC), charger offering three stage charge profiles as well as an AC and DC distribution center. It must be wired for AC-In to run the converter/charger and feed the AC buss. Then wired out for AC out (from the breakers you mount on the AC buss) and 12V DC-out to your loads (lights, water pump, refer, etc.) AND ALSO the CHARGE circuit must be wired to the battery. All six DC outputs look like 12V out however only five of them are designed to handle loads and ONE of them is your 3 stage charger output. Green-Blue-Brown-Grey-Yellow are your 12V LOADS each fused on the front panel of the WFCO with the appropriate size fuse. RED is the sixth fuse down from the top and is your CHARGER wire and should be fused according to the output of the WFCO your using (in my case 30amp). The 7th fuse down from the top is your reverse polarity fuse (40amp).
It sounds like you have load items wired to the CHARGER (red wire) portion of your WFCO which is wrong. The RED wire from the WFCO goes directly to the battery positive (no in-line fuse required as it is fused in the sixth position on the front panel of the WFCO). Whatever loads you have tied to the red wire should be tied to one of the unused FIVE 12V load wires (or split to multiple unused 12V load wires).
This is the inside cover of my WFCO (guessing same as yours)
I have labeled all of my FIVE 12V load wires on the front panel next to the fuses;
On the back side of the WFCO you can see I've tie wrapped all of the 12V load wires together and the RED charger wire goes directly to the battery;
Here you can trace the RED charger wire out of the WFCO directly to the battery positive;
Lastly my AC distribution I've split into four breakers (not using all right now);
I hope you can sort this out. If not, PM me and we'll pick a time to talk.
Dan