I have the same issue. Cleaner tool does not hetl, at least in my case. Do you mean that the whole CS5.5 Master Collection should be uninstalled? I have tried everything else:

1. I tried to uninstall, but Flash Builder was not listed among the programs, maybe I have uninstalled it earlier or it is inclkuded in CS5.5
2. I deleted all Flash Builder related files, no help
3. Then I deleted all Flash Builder related registry entries, no success
4. Finally I downloaded the cleaner tool, its action options do not include anything Flash Builder Releted.

I simply can't get rid of the conflicting version

Same problem here. OSX 10.7.3, all old versions of builder were uninstalled, cleaner tool showes nothing builder related.

I had been struggling with this issue for days and no one seemed able to help me, changing the file names solved it.  Thank you!

Thanks, this approach worked.

After installing it, rename the files back to be able to uninstall/upgrade the other products.

On mac it is in library.. which is hidden

so shift command G, or Go, folder

/library

you should have a finder window open in library now.

application support

adobe

caps

Those are the installation.. logs, sorta.

So when you install a product, it will write to those files.  I am guessing previous versions did not remove itself properly from those files.

What I would do on that, is after you install and it creates those two files, prefix the files with fbcs6- and then rename the others so you can modify/remove cs6 and other software.  When the day comes to remove flashbuilder cs6.. rename again.

This of course is a workaround, not a solution, perhaps adobe will create a utility to go into those files and clear out the erronous entries.

Another work-around I found is to install in Trial mode then activate your license after the install. I finally chose Trial and the message didn't come up.