There could be a few issues to cause what you are describing.

For one, the charge solenoid may have failed, so the second battery is not charging. If you have gotten rid of it, then that already solved that problem!

Another possibility is that, with the "different" routing of the cable through the wake plate...you may have some odd items on odd batteries. The normal mode would be to have the stereo and non-essential items on the secondary battery. The engine run, gages, starting and bilge should go on the primary battery. Anything else is pretty optional, like wake plates and ballast pumps. The PO could have done, literally, any combination.

Finally, with the indirect battery cable routing, you may just have a poor connection somewhere causing the issues.