Hi Peter,
welcome on forum.
I have doubts that this is CRLF, probably only LF, because CRLF is handled correctly and you would see two boxes for both chars if it is CRLF.
That works when you copy it to editor, because it recognizes all combinations of line breaks and can works even in mixed mode, but this is not implemented for Output Window which currently uses normal edit box for displaying text (this would be changed next versions).
Can you please send me (Bug report entry in Help menu) file created in HippoEDIT from the output text, then I can check what is really read.
You can also see this by yourself:
check View->Editor->White Space, then you would see real line endings for the output text (if it is mixed).
Also in the status bar should be written which type of the line breaks is used.
I can try to fix this, by replacing all non-dos line breaks by \r\n, this can decrease performance a little bit but I think would not be noticeable.
Would try to do this next 1.47 beta, but please check that my assumption was right.
Best regards,
Alex.