If this has happened to you, don't wait for Smartertools support to fix it for you. Use SED (cygwin, or rktools, etc), or any other search-and-replace tools to edit all your config files.
The config files for each site are found, normally, in C:\Program Files (x86)\SmarterTools\SmarterStats\MRS\App_Data\Config\Sites. Make a backup of the files, then change the following line:
...in all the *.xml files. Then, restart the smarterstats service, all will be back to working normally. I used the command line For and SED commands like this:
for /r %%i in (*.xml) do sed s/"UncUseSystemDefaults>False"/"UncUseSystemDefaults>True"/g %%i>%%1x
This left me with all the same files with a trailing "x"...some simple copies/renames, etc, got me back all my xml config files with the UNC setting set so it uses the default login...like it should have after the upgrade.
I believe this was an oversight by the smarterstats development team...and, granted, most users do not use the UNC option...but we did.