MadCompie:
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This script simply takes each line and strips the trailing spaces.
To simulate, select some 2000 lines in a text file and apply the script. It will
take some half a minute...
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Testing with 75kB Java script code. It was executed immediately. I added echo
before and after the last seltext and there was no delay.
Maybe something in settings. 
How long are lines in your code?
Can you send me your PSpad.ini, I can test it with your settings

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