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 :(
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