I was thinking about that after my post. No, I haven't noticed the pixel shift in years but I think it may be because of the habits I learned to export the bitmap files. I have far more issues with reflections.
If you still have a skin source file that has shifted pixels, I'd be curious to hear if the offset shows when those files are placed in a terrain's texsrc folder and built. The terrain wouldn't need to be uploaded as your local build engine is the same one used to create the terrain on the server. If the corrected versions of the bitmaps then show correctly, it would provide a utility for testing different export settings in other programs and potentionaly shortening your process.
After I've create the particular texture, I create a 'New (layer) from Visible', then select the layer, Copy All and paste as a new GIMP image, Ctrl+Shift+V. I just don't bother to save this temporary 'file' to the HD. If saving a grayscale, I delete the alpha at this point, which you never want to do to your original source files. If a Diffuse, I then export the new unsaved image as a bitmap, but under Compatibility Options, I check Do not write color space information. The default Advanced Options are for 32 bits A8 R8 G8 B8. Some of the terrain related bitmaps can be either 24 or 32 bit, so there's that.
As you said, the best tool is the one you're most familiar with. I'd be lost with either of the two other popular programs mentioned.
