Changing/replacing textures causes the correct alignment of the texture to be lost. I need to replace textures in order to handle import/exports but replacing them in program causes the following to happen: (Please see the following gif animation of screen capture)
http://i.imgur.com/KOkX4Xt.gif

The only workaround to avoid this misalignment when replacing textures that I've worked out is to export to collada .dae, open the file in a text editor and manually editing the path to the new image file.
http://i.imgur.com/cJ3teSY.png

Hopefully you can fix this 
Best Regards
Nicklas
http://nirklars.wordpress.com