I just downloaded the free version and tried the code cleaner on a small page of code. I wanted it to indent and on auto nothing happened. When I adjusted the indent it came up with an access violation.
fully licensed XP prof all updates.

Am I doing something stupid?

Other than that, the program runs fine?
I ask because sometimes the instal of a program does not always go smoothly. I have used the code cleaner many times with XP home and it worked nicely. Try changing the value of the indent back to the default setting and see if it works again, then try different values.
I would also try to instal the program again. Maybe a file got dropped somewhere in the first instal.