Battery was at 6.25v - is that a 6v battery or a 12v battery? If it's a 6v - well and good, but if it's a 12v battery it's likely to be toast.
Is it a flooded type battery where you can add water, or is it a sealed type battery? If it's a sealed battery and you smelled fumes from it venting - well that's that. It's all downhill from there. Sealed batteries have a pop-off valve to release over-pressure in the event of overcharging but there is no way to replenish the lost water, so it will forever more have a dodgy electrolyte balance.
Even if it's a flooded battery, and you can top it off with water, it's likely to be unacceptably (and permanently) weakened from too long a period of not having been properly charged.
You will probably have to replace it. If the battery is in your living quarters, then you should replace it with a sealed battery. A true "deep cycle" (NOT rv/marine) AGM battery is the best.
Starting batteries have thin lead plates to dump peak amperage quickly, deep cycle batteries have thick lead plates to dump sustained amperage over a longer time, and RV/marine is a compromise between the two with medium thickness lead plates.
AGM (Absorbed Glass Mat) is a sealed battery that has fiberglass matting between the plates. They don't vent unless overcharged (like any sealed battery), and they don't slosh because the electrolyte is absorbed into the matting.
I would avoid Gel type batteries, as they desire a slightly different charge voltage and are very sensitive to being over-charged. They require a charger that has a "Gel" setting. AGM and FLA (flooded) generally have the same charge specs, so a charger that works on one, will work on the other.
If you replace the battery with a flooded type (you can add water) then if it's in your living compartment, you should ABSOLUTELY put it in a box which is vented to the outside and CANNOT vent hydrogen into the living compartment. When hydrogen burns, it's somewhat like gun powder - it burns so fast, that to the naked eye, it's basically indistinguishable from an explosion.
Technically, even a sealed battery is supposed to be in a box vented to the outside - "just in case" it gets overcharged and the pop-off valve releases hydrogen.
As to the Magnetek...they don't have a very good reputation. They were apparently a low-cost unit favored by many RV manufacturers at one time. Favored due to the price, not the performance. Apparently the 12v converter/charger section is not a very good design.
There are many reports on the Information SuperInterWebs Highway about Magnetek problems and failures.
Parallax Power makes an upgrade kit for the Magnetek 6300:
http://www.parallaxpower.com/7300/7300RU.pdf
BestConverter.com sells the upgrade kit.
http://www.bestconverter.com/Magnetek-63007300-Upgrade-Kit_c_64.html
The upgrade kit comes with either a 45a or 55a converter/charger section (more output than the original) and a new fuse block (to handle the increased output), and is reasonably easy to install. Here's a page on BestConverter.com that shows photos of the process:
http://www.bestconverter.com/MagnetekParallax-to-Ultra-III_ep_8-1.html
Personally, if I were to go that route, I would go with the 45a unit. The reason is simply that a 55a charger is right at the ragged edge of what a common "1600w continuous / 2000w surge" inverter generator (such as the Honda, Yamaha, Champion, Kipor, Briggs & Stratton, Generac and others) can run. 45a is right in the sweet spot to run from a 1600wC/2000wS inverter generator - 55a is pushing it. The Honda could almost certainly handle it. The Yamaha probably. The others...roll of the dice.
Another option, is to replace the converter/charger section of the Magnetek with a different converter/charger entirely. Here's a page on how to replace the 12v converter/charger section of a Magnetek power panel with a Progressive Dynamics converter/charger:
http://home.comcast.net/~rabarber/magnetek.htm
Here's a page on replacing the Magnetek converter/charger section with a 55a WFCO converter/charger:
http://homepage.mac.com/pseabolt/Camper/Converter web/Site/Welcome.html
Personally, if I were going to go that route, I'd probably use an Iota DLS converter/charger with IQ/4 3-stage control module rather than the PD or WFCO:
http://www.iotaengineering.com/12vdc.htm