motorsep: Unfortunately, textures alignment is very sensible to what transformations are applied to UV-coordinates. In NetRadiant only three are allowed: position, scale and rotation. If one made even very little shift transformation result may become surprising. I believe this is the case you have met.
And I have no idea on how one may solve this problem. Actually there is one idea: make texture file with transformed image for each face but it's relatively big work and there would be as many texture files as faces in mesh.
halogene: I usually restart Blender to get changes applied. Oh, man, give me your had on a plate!

One should copy only "./exporter" subfolder contents to "./blender/scripts" the rest of files and folders contain manual and example files. There is a mnemonic rule how to determine correct folder to copy: it should contain *.py file(files) and "bpymodules" subfolder.