I am sure the site is pointing to the correct database :)
Do you use Alloy templates (or rather do you compile against EPIServer assemblies somwhere outside bin folder)?
In that case you need to either remove or change the config transformations and copying form libraries folder before compiling.
My guess is that you comipled the project after upgrade and during that compilation it copied folders from libraries (or similar folder where EPiServer assemblies are located) and hence the updated assemblies where overwritten with old ones.
Did you ever find a solution to this? I'm having the same problem after upgrading a site from 7 to 7.5.
I have installed both EPiServer CMS 7.0 and 7.5 on my development machine. When I tried to upgrade our site from 7.0 to 7.5 I get an error when running it:
"Dynamic Data Store 7.0.859.1 can only be used with database version 6207, current version is 7000. Make sure both database and assemblies are upgraded correctly."
The database is upgraded to version 7006 but the EPiServer assemblies are still in version 7.0.859.1. Is it because I have both 7.0 and 7.5 in my machine?