With NO plug-ins active and .htaccess recreated, the ONLY way my Categories and Tags (and lists thereof) will work IS with the DEFAULT permalink structure. This, of course, propagates irreparable linkback issues. It’s a very temporary workaround.
Further, setting the optional Category and Tag permalinks has no impact. It’s this is the same situation on THREE installations … two are MU activated.
In searching for a solution, I’ve found over 100 posts about this issue … on wp and elsewhere. That means at least 1000 people have the problem and are reading comments from others.
I can imagine many people getting scared about upgrading after this ordeal.
I don’t ever recall a single upgrade creating the exact same MAJOR pblm for so many folks. Is there a hotfix for this calamity?