I have seen this too once I upgraded to 3.5.0. However, each time I go to the "immunize" tab, it says there are 10,918 unprotected items (and 0 protected items) for firefox. I can go through the immunize process without problems it seems, but once I reopen spybot it shows 10,918 items as unprotected for firefox again. The items are shown as protected for internet explorer which is the other browser I have on my system.
Has this been documented by any other spybot users?