Oh wow, you're right, it isn't there. I'll add it in, it should be there.
Thought I replied to this long ago, but I guess not. The SNES version is shorter by 1-2 minutes for the US version and 2-3 minutes for the JP version, as the JP version not only has no load times, but also restores much of the missing health throughout the game, as well as being generally easier all around. The reason the Genesis version has lower times is because it's the only version that has anybody doing serious runs for it.
It was because the difficulty option was set up, but not flagged as a subcategory and because of that the leaderboard was only displaying original difficulty runs with all others being hidden. Subcategories are now showing correctly and your run should appear.
After a lot of trial and error, a few of the annelids and I have discovered that the GOG version of Jim 3D is complete trash. Just look at my ~4 hour run to see examples of how choppy it runs, then look at any of my recent runs to see how much better the original release runs. A few major examples off the top of my head are:
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DXWnd doesn't work for GOG release, meaning there is no way to play in windowed mode.
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The original release runs at a much higher and smoother framerate than the GOG version.
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The GOG version choppiness causes moving platforms to glitch and have weird physics. For example, Jim will randomly hover in the air while the elevator continues down (Especially in the elevator in Are You Hungry Tonite), or clip through the floor while riding elevators up, and In Death Wormed Up Jim will slowly slide backwards off the moving platforms if you stand still, neither of which happen in the original release.
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The GOG version often will drop inputs because of how choppy it is.
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The GOG version crashes much more often.
I haven't played the steam release, but from the reviews it sounds like it has a ton of problems as well.