Sorry for the delay in response time.
I'm running an update of Firefox 2, not a clean download. I looked for the file "permissions.sqlite" but it was not there. I tried deleting just the "hostperm.1" file and following the instructions after that and ended up with about 6000 unprotected and about 5000 protected. The unprotected files were all of Firefox cookies, images, installations and popups.
I restored the hostperm.1 file, so everything is the same as it was when I began this thread. There are now 54558 unprotected files and 64903 protected files.
Emerald,
When one starts with an XP-HOME SP3 system that has never had Firefox (any version) installed, but does have the Spybot 1.6.0.30 or 31 installed, and Firefox 3.0.1 is then installed from the Admin account (default standard recommended installation) the following is observed.
At the end of the installation and after an initial open of the FF3 browser, the permissions.sqlite file is found at C:\Documents and Settings\username\Application Data\Mozilla\Firefox\Profiles\fnwb3fgn.default and it is 2k.
A Spybot immunise can then be made and works correctly, resulting in the permissions.sqlite file increasing to 931kB.
If one deletes this permissions.sqlite, and then runs Spybot and an immunise, the immunise will not work on the Firefox items, however it will cause another permissions.sqlite file to be generated - its size is 0k.
If one deletes this permissions.sqlite file, then runs the Firefox browser, it will generate a new permissions.sqlite file, this time 2k, the same size as the original, and one can then immunise correctly in Spybot.
At no stage is a hostperm.1 file generated, because the hosperm.1 file is relative to Firefox 2, not Firefox 3.
I believe the solution to your problem is to uninstall Firefox 3 completely, and to remove any files or folders it may leave orphaned. In particular if there is any Mozilla folders in C:\Documents and Settings\username\Application Data\ then delete them.
If you don't already have Spybot current version 1.6.0.30 or 31 installed, uninstall the Spybot version you do have completely. Then download and install the current version.
Once this has been done, re-install Firefox 3. Check the location of the permissions.sqlite file and it should be as given above. If for some reason its size is 0k, you could try priming it by manually adding a couple of sites that cookies should be accepted from. (Open Firefox, Click on Tools, then Options, then Privace, then under Cookies click on Exceptions and type in a couple of Web site addresses and for each click on Allow. then click on close, then OK. Shut browser, check that permissions.sqlite is now larger than 0K, then Immunise.
I hope this helps.