My Textpad is configured to "strip trailing spaces" when saving. So some extraneous content, invisible, apparently existed on random lines.

Trailing spaces should not make any difference to line numbers.

I suspect that Textpad actually fixed some end-of-line problems as everyone else has suggested might be the cause.


FYI I use Activestate's Komodo Edit for my editor (it's free), but it's not a proper IDE like Padre.
Activestate's Komodo IDE is a proper IDE, but it costs $295 :(
http://www.activestate.com/komodo-edit/downloads
http://www.activestate.com/komodo-edit/compare-with-komodo-ide