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I have a similiar problem using a macro. I select an entire line (shift+end), F8 and replace with a space in all open files. Works as expected when used manually. The macro version only moves cursor the the line end. Based on other posts it seems that both regex and macro implementations are buggy ...

I experienced the same issue. After some playing around it seems that registry settings have been moved to xml files. These are found at C:\Documents and Settings\username\Application Data\Helios\TextPad\6\ConfigState.xml and GUIState.xml. Also these files do NOT get updated until you exit TexPad ...