When I place the lever at a distance from the Classic Jeb Door and turn the power off, the middle pistons don't retract until the side pistons retract, making the whole thing not work. When I took away the repeaters and extra redstone, I see that the middle pistons don't retract at all. However, this bug only happens when the lever is at a distance from the Classic Jeb Door.
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This is probably MC-11193, one of the bugs that's extremely complicated to fix and is a side effect of the way redstone is implemented. (One indication of this is that it varies by the lever's distance). You should be able to solve it by putting repeater before the 2 redstone dust in the middle of the door.

The Classic Jeb Door didn't always have this problem. Did one of the updates throw it off?

The thing with MC-11193 is that it depends on a lot of weird system-dependent properties, including your Java version and distribution (and also, where you build the door, and in what orientation, among other things). So you can run into it randomly without expecting it.

Ok then, I will use an extra repeater for my future builds with the Classic Jeb Door. Thanks for the help, and I hope the bug is resolved soon.