When a transform is added currently it is inheriting the Build Action of the original file. This is not the correct behavior, they should instead be added as None.
Sorry, should have added this issue myself! :-)
This should be fixed with commit 765086e. I have built a new version of the VS add-in and its available at https://dl.dropbox.com/u/40134810/SlowCheetah-765086ef27.zip. I would appreciate it if you could verify the fix. I will close this item now, but if you find that its still an issue re-open it.
Uninstalled old version, innstalled your dropbox version. And I'm happy to say, this works now on my machine.
Cool thanks, it will be included in the next release. Perhaps next week or so, I need to fix a few more bugs before I push it out.
The fix to this has been released at http://visualstudiogallery.msdn.microsoft.com/69023d00-a4f9-4a34-a6cd-7e854ba318b5/.