It sounds like the import wizard did not run as expected, which was a bug in 1.6 that was fixed in 1.6.1.
Delete the Profiles folder found at C:\Users\$USERNAME$\AppData\Local\MatterControl\Profiles (AppData may be hidden by default) and relaunch 1.6.1.
This time the import wizard should run and you'll be able to import all the settings and profiles from before the upgrade. Once you have those I suspect that slicing will work as you expect.