Ask such questions in the LR forum. Anyway, by default it uses the system file associations, so it would appear you nbeed to fix those...
Moving this discussion to the Photoshop General Discussion forum.
This may not be the only way to have fixed it, but here's what I did. I uninstalled Lightroom. Then I renamed the Photoshop CS4 and CS5 directories by just adding an extra hyphen somewhere. Then reinstalled Lightroom. Since the installation program could no longer see the Photoshop CS4 and CS5 directories under their proper names it located the correct CS6 directory and all was well. Problem solved.