Steps To Reproduce:

1. Mount folder in Files Tab
2. Browse to file, then right mouse click on file and choose "Open In..."
3. Select the Server "MySQL 5.1 - 37"
4. Query Window will open with file, and the database combo box will indicate that "aquatest" is the current database.

This is incorrect.  The current database context is "mysql".  "aquatest" is the first database on the list, and probably just selected as default.

Correct behavior :

1. In Schema Browser click to select "MySQL 5.1 - 37".
2. Click Query Analyzer to open new Query Window.
3. You can see that the database combo box shows "mysql" and the database and not "aquatest"