PAL 25 fps conversion to 24 fps.

PAL is shot at 25 fps. Not sure why you are seeing that message from Cinema Tools.

Why do you feel it is neccessary to convert your video to 24 fps? Unless you are going to transfer it to film for projection, I can't really see a good reason to add this step to your workflow.

If your intention is to achieve a more cinematic look to your movie, then changing the field dominance to progressive will do that to some extent. This is very simple to achieve in Compressor.

To go some way to a more cinematic coloring, this tutorial may be of some help:
http://www.kenstone.net/fcphomepage/film_lookrevisited.html

There are also several other articles on Ken Stones very informative site, searching for "film look" turned up over 500 results, while searching for the article linked above.

Well it tells me the footage is not 25 fps.
This news to me as the camera is set to to PAL and I thought PAL is shot at 25 fps?

PAL is 25 fps. It's possible that you made a mistake somewhere along the line.
Open the original media (inside the Capture Scratch folder) in QuickTime Player
and choose Get Info. Is the framerate 25? If not, then you captured it incorrectly
or you accidentally changed it.

Cinema Tools works great for conforming, but if you try something, it will
save to the file without asking you. Maybe that happened while you were
experimenting.

So I selected a scene in the time line and choose conform 25 to 24 in tools.

To conform you need to select the clip in the Browser, not the Timeline.
If you conform the clip, then the file gets changed, so every instance
on the Timeline is changed.

When you've got your 25 footage conformed to 24, you'll notice that the
sound is pitched lower, so you'll need to change the pitch of the sound track + 4.17%.

Of course, the question remains: does it look "nicer"?