I should have been more precise: The offsets are only clamped when you use the auto-alignment tool or change them manually in Visual Mode. When you move an aerial middle texture, the Y offset is exempt from this. You do need to explicitly target the middle texture with your cursor for this to happen though. If you target the lower or upper texture and move that one, the offsets will be clamped. That can indeed be annoying and I'll try to change it. Apart from that, I can't think of a situation where you can't produce a unique offset configuration because the offsets are clamped.
Plus Visplane Explorer tries to activate every time I install Zone builder or a zone builder update. The only way I can deactivate it is to delete it.
I'm not sure what you mean by "tries to activate". The Visplane Explorer should be disabled by default. If it isn't, you can go to Game Configurations -> Modes and disable it there. But even if it's enabled, I'm not sure why it would cause problems as long as you don't use it...
Edit: Noticed a bug. Things are colourmapped/darkened based on their Z height relative to the sector floor. Which doesn't look right when you have flipped Things in a sector partially filled with a colourmap or different sector brightnesses. (The colourmapping-ness of Things ignores whether the Thing is flipped or not.)
Fixed.
As for glaber's alignment bug, I've identified the issue: When using the Lower Unpegged flag on a lower texture, the texture
should be attached to the lower floor. Instead, Zone Builder displays it as being attached to the ceiling
above that floor. You can easily observe this in Visual Mode: If you move the floor below a texture with Lower Unpegged, the texture will stay in place. If you move the ceiling above it, however, the texture will move along with it.
Now here's where it gets weird: This isn't a new bug. It also seems to happen in all previous versions of Zone Builder, in GZDoom Builder, in Doom Builder 1 and 2, and in SRB2 Doom Builder. Weirder yet, it also seems to happen in SRB2's OpenGL renderer. Only SRB2's software renderer and Workbench's 3D mode display it correctly. Unfortunately, that kind of limits my options. I barely understood enough of the rendering code to port the OpenGL texture skewing code to Zone Builder, but I don't understand enough to identify an issue that exists in
both SRB2 and Zone Builder. I filed a bug report for it, but until someone fixes it in SRB2, you'll have to live with it in Zone Builder too, I'm afraid.