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The mouse sensitivity is higher vertically for me than horizontally, which feels very uneasy. That goes for both Thief Gold and Thief 2.

Are there any tricks to fix this?
That was/is on the ddfix to-do list, but I never got around to it. An external utility is your best bet.
I ran into this issue a while back when I tried installing my old disc version of the game, but I haven't heard anyone on GOG mentioning this issue. Does the GOG release also have this problem? If so, how are people dealing with it?
I have the GoG version, that's why I am asking here.

Right now I use a Razer Diamondback 3G mouse and I can lower the Y-Axis mouse speed in the software, but I mostly use a Zowie AM which has no software and I was not able to deal with this problem.

So I take it there is no fix for that yet?
Psychomorph: I have the GoG version, that's why I am asking here.
Interesting... I would have expected to hear more people discussing the problem on these forums, but this is the first topic I've seen about it. Does it only happen in some cases? Do other players have normal mouse behavior?

Unfortunately I don't know how to fix it, but if other players don't have the same issue, maybe we can narrow down the actual cause.
I believe it's to do with ddfix's widescreen, as it doesn't need to present itself when I run a non-patched version of Thief Gold.

I also find that mouse movement with ddfix installed becomes much more jerky than it is on a vanilla install. Sadly, I don't expect ddfix will be getting any more updates to fix these issues.