You can change the Y texture offset, but not the X offset.
This is a known (and old) bug in SRB2. See here:
http://mb.srb2.org/showthread.php?t=33899.
- EDIT -
There is a workaround you can use, though! =)
- Do not use the texture from the control sector of the FOF. In fact, make the FOF one with no sides (search in the FOF linedef specials).
- Set up individual middle textures in the target sector lines, and give each one a distinct X offset.
If it makes sense in your situation (judging from your picture, it seems to make sense), give the target sector lines the flag "Lower Unpegged" in order to bring all the middle textures to the ground.
- Adjust the Y offset of all the middle textures to align them with the FOF's floor and ceiling.