Hi,
I have the same "problem" before.
But most time its occured by use different tabsize and difference font and fontsize.
Non monospaced fonts are scaled not proportionally and AkelPad's MaxTabWidth equal to SpaceWidth*TabSize other programs may calculate tab width differently. Try replace tabs with spaces and compare results.
Have you set both editor's tabsize be a same value and use the same font(monospaced font is Recommended) and fontsize?