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I'm trying to click on the error messages in the output window to go that line with the error in the Python file. This is what the line in the output window looks like:

File "H:\Database\Python\read-from-text.py", line 91

And this is my RegExp to match the output:

File "(.+)", line (.+)

And it works, IF the filename is the same file that was active when I executed the tool. But if it's a different file, nothing happens. Even if that file is also open in Textpad.

1) Posix: in Preferences/Editor [X] Use Posix regular expression syntax ??
Otherwise your RegExpr should look like
File "\(.+\)", line \(.+\)

2) I assume you did not forget to set the registers (drop down lists below RegExp Textfield) correctly
=> in your case
File: 1
Line: 2
Column: <empty>