Texture alignment issues
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When changing texture offsets (either manually or through the auto-alignment tool), the offsets are clamped so that they don't exceed the height/width of the texture. This is useful normally, but it should ignore multiples of 4096 on repeating middle textures, since they determine the number of repetitions. -
http://mb.srb2.org/showpost.php?p=779946&postcount=162 If you use a vertical offset on an infinitely repeating middle texture, the texture will only tile upwards/downwards from the point it's pegged to. Zone Builder currently ignores this. -
Lower textures behave incorrectly when given the Lower Unpegged flag. They seem to be pegged to some fixed global height, rather than the lower floor as they should. -
Report of the auto-alignment tool producing incorrect alignments when lots of FOFs are involved: http://mb.srb2.org/showpost.php?p=776930&postcount=119