Are you logging in from the same computer every time? The game saves a local file that stores the position of all the items; if you log in from a different computer it won't be able to load it and will default everything to the middle.
Does it happen every time or just some times? If it's a problem every time you log in, then you might check that you can write to the ProgramData directory, for howlbreath it's at: C:\ProgramData\howlbreath\. When the inventory configuration is working correctly, you should have a ".bagcfg" file for each character in that location. If it doesn't occur every time, then it's likely a bug in the client -- if this is the case, any details on when you do/don't see it would help us reproduce so we can fix it.
We didn't change anything in regard to the inventory locations, so I would expect the issue remains.