Have you tried to deactivate all plugins? Cleared all caches?
yes, but nothing… even I contacted my host provider (rackspace) without success, they told me that even they found the same trouble when they try it to update to 3.9 in a test environment
Same problem. I have also updated to 3.9 now. Still have to update the permalinks a few times a day. the 404’s go away for a little while(like 4 hours) then the 404’s return.
this is not fully solved but at least is working properly:
the problem was Sucuri Security – SiteCheck Malware Scanner plugin that working together with WordPress MU Domain Mapping create that 404 error. now what I have to do is:
if I want to enable permalinks is deactivate all the plugins then activate permalinks, then enable all except Mu domain mapping neither sucuri plugin
once is done and verify I activate MU domain again… maintaining sucuri plugin disabled.
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