[Coulomb]

I also noticed that under 110v I need to have the hot leg in a specific position for it to work, which seemed odd at the time.

It sounds like one of your hots isn't hot. So perhaps it's operating at 120 V when your are expecting 240 V. Check your outlet and/or wiring.

There are two charger "units" in there, but as far as I know they'll just be in parallel (both inputs and outputs). I'm not familiar with how split phase affects this; I would expect it would not affect the charger wiring at all.

Edit: there are input (AC), and often but not always output (DC) fuses. The output fuses rarely blow in my experience. When the input (240 VAC) fuse blows, it's often a sign of trouble, but they occasionally fail through thermal fatigue. Also check the pre-charge resistors (2 x 150 Ω in parallel) and the input relay.

I can't recall seeing one of these chargers with yellow and red mains wires; they've always been black and white. It could be a north American thing, even though black and white are also a north American standard.

 

[Coulomb]

I think I found the problem. ... So, I was feeding one hot leg in (red) and returning through ground, which is a bad idea.

I haven't hooked it back up yet...

Please check very carefully before powering it up. The way you thought it was seems it would have connected a hot to chassis, which you should have noticed painfully, and returning through ground should have tripped your GFCI, I would think.