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Originally Posted by stickyfingerzdotnet
Only thing I can think of is you somehow entered the wrong domain name when updating. But that is kind of doubtful.
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Nope. I even deleted one of the blogs and started from scratch. Last night before I went to bed I reinstalled WordPress on one domain and it looked fine. When I woke up, it was messed up again (wrong domain links on the blog and redirecting me to the other blog when I went to admin)
It doesn't make much sense seeing how they're using different databases.