Ok, I know the cylinder itself isn't wonky, but something is. Passenger side cylinder was bad, driver side is fine. Followed Fishers instructions to replace the bad one, including putting the top up to do the repair. Removed old cylinder, installed lines to new one, and pressed the top "up" button to extend rod to full length so I could finish connecting. All per Fishers manual. Rod would not extend.
However, when I pushed top "down," the rod started going UP. Meanwhile, the driver side is doing what it's supposed to and trying to pull the top down. Because of the length and placement of the lines, I could not have connected them differently on the new one than the old one. There is definitely air in the lines, but there's got to be more to it than that. Aside from what causes the yin/yang, is it fine for me to just extend the replacement cylinder rod to full length before installing?

 

Perhaps no one responded because they realized I was a moron, like I did last night. Despite how confident I was that the lines were hooked up properly, I obviously switched them. Once I switched them back all was fine. Now I just have to figure out whether I have to do this all again because the replacement cylinder I got is leaking very very slightly from the top seal where the rod comes out. We'll see how long it takes for it to start struggling on that side

 

I switched both of mine by mistake and for a while had to push down to bring it up. Finally switched the wires at the motor plug because that was the easiest way to make it correct.