So the results are in, and now i am more confused...
With filter out of the system:
The New battery ran for 2+ hours right out of the box. It charged up to just over 29V and ran for 2+ hours for a few days.
I then put the filter back into the system. This returns me to the original setup, but with the 3rd battery installed.
To my surprise he stills charges to over 29V and runs for 2+ hours.
I guess with those results it must have been something up with the 1st 2 batteries...
I will continue to keep on eye on Bubba, but i guess he is all back to normal. (or so it seems!)