In notepad++ I have set "replace tab with 2 spaces".
When coding in python I copy-pasted some code from the web and it appeared indented correctly. But running the code resulted in indentation errors, which I solved in the end by removing all "visible" spaces at line beginnings and inserting the same amount of spaces again.
Could it be possible that scintilla based notepad++ does not show all special chars but displays them as spaces? Is there a setting to fix this?
Have you tried setting the menu command View->Show all characters, or View->Show White Space and TAB? (Running notepad++ V5.1 here)
You could double check your text with the Hex Editor Plug-in. In your case there may have been some control characters which have crept into your text. Usually you'll look at the whitespace, and it will say 32 32 32 32, or for unicode 32 00 32 00 32 00 32 00. You may find the problem this way, providing there isn't masses of code.
Download the Hex Plugin from here; http://sourceforge.net/apps/mediawiki/notepad-plus/index.php?title=Plugin_Central