You are right, the macro is not working anymore. I tried the macro on your example with several versions of UltraEdit and found out that it does not produce the correct result from UE v126.96.36.1990 to v17.00.0.1035. Previous versions like UE v188.8.131.521 or v184.108.40.2066 produce the correct result.
When executing the 2 replaces manually twice with Selected Text selected for Replace Where, it also does not work. After the first replace the modified lines are highlighted still as they would be still selected, but that is not the case as it can be seen when moving the caret with UP/DOWN ARROW or pressing Ctrl+C (copy) and Ctrl+V (paste).
Interesting is that running first replace with Current File selected for Replace Where and second replace with Selected Text, the second replace works. Of course that is of no use for you and works only on this small example.
This is definitely a bug in UltraEdit. I have reported it to IDM support by email and IDM could reproduce the wrong behavior.
By the way: Using
Find RegExp SelectText "^//([0-9A-F\?]+).*\r\n"
Replace All "$1"
makes the reformatting job in one replace, but requires that always entire lines are selected. And of course does not remove the DOS line terminators on lines not starting with one of the characters defined in the square brackets.
Update on 2011-06-03: The problem with selection discarded after Perl regular expression replace all on selected text is fixed in UE v220.127.116.118.