Hello,
we have today checked and revised SOBI2 extension with the latest SOBI2 version released. (downloaded yesterday, version RC 2.9.1.0)
It seems to be working correctly.
We tested all category-related settings (add no category / add last category only / add all categories).
All entries and categories are accessible.
Please, make sure to clean or disable cache in SOBI2 configuration.
Also, clean JoomSEF cache.
You may try to upgrade to SOBI2 extension version 2.0.1 as well, although, there were no major functional changes made, just a small cosmetic caches.
I think, most likely, the problems might be connected to SOBI2 cache. So, please, try to disable it and test again.