Whether it is an upgrade from a previous version or not is irrelevant. ALL Adobe upgrades are FULL INSTALLERS. They do not need nor touch any previous version. If they don't find a prior version install, they will simply prompt you for the old serial number as well as for the new one.
As far as your issue, please do a forum search on the keyword Yosemite.
If you installed Yosemite after Photoshop was already installed, the Yosemite install damaged your CS6 installation. Now you must uninstall Photoshop, re-install it, and apply all available updates.
If you perform the forum search I suggested, you will see that many users are being advised to downgrade to Mavericks,
Make sure you install the MacOS 10.10.1 update.
And you probably should install the WhiteWindowWorkaround plugin as well: Menus, shortcuts, Lasso tool, or Photoshop stop working when using a Wacom tablet | Mac OS
I've updated Mac to 10.10.1 as you suggest. Brushes in Photoshop seem to be working OK now. Would there be any benefit in installing the WhiteWindowWorkaround plugin, could it cause other problems?
I had the SAME issue as the original thread. Really bad lagging with my tablet in PS CS6. I was running the latest driver from wacom and Yosemite 10.10. After updating to yosemite 10.10.1, the issues were gone. The wacom tablet worked perfectly again.