Beat, when using the Edit In CS5 option there is a similar dialog with the 'stacking' option, but only for non-RAW files. For RAW, I had thought that stacking is always assumed as I couldn't find a way to say that I don't want the Tiff/Psd stacked with the original RAW.
However, have just discovered something that may be what's causing the problem here, so an independent verification would help:
1. Using "Edit in CS5" on a JPG, and uncheck 'Stack with Original' and when I click Save in CS5 the Tif is returned alongside the JPG, but not stacked....as expected.
2. Repeat using a RAW file, thus no option to select/deselect stacking, press Save and Tif is returned alongside the RAW, but not stacked.
3. Repeat 1, this time select "Stack with Original" and the Tif is returned and stacked, as expected.
4. Repeat 2, and hey presto, the Tif is returned and stacked.
Conclusion: the "Stack with Original" option, although only available with non-RAW files, is "sticky" in relation to RAWs.....so whatever you had the option set to the last time you edited a non-RAW file is the option you get when you edit a RAW.
Paul, suggest you try an "Edit in..." on a JPG, select "Stack with Original', then try the same on a RAW and see what you get.