Can you please try this:
1. Close any instance of TheBrain or PersonalBrain you may have running.
2. Open Terminal
3. Copy and Paste this (one line at a time):
defaults write com.apple.Finder AppleShowAllFiles TRUE
4. Navigate to: (/Users/YOURUSERNAME/)
5. Delete any .PersonalBrain folder if one exists and you are no longer using or no longer have PersonalBrain 6 or lower installed.
6. Navigate to: (/Users/YOURUSERNAME/.TheBrain)
Another way of getting to this folder is by right-clicking on a Thought in your Brain and selecting 'Add Attachment' then 'Templates...'. This will prompt you to open the folder associated with Templates. Select 'Yes' and the folder will open. Navigate one level up in the folder structure and you will be in the .TheBrain folder.
7. Move any .xml and .bak preferences files to your Trash.
** Please Note that this will remove your current preferences so you will need to log in to TheBrain application again and manually open your local Brains by navigating to: File > Open Brain...
8. Empty your Trash
Once these steps have been completed please try restarting TheBrain.
If you wish to hide hidden files again:
1. Open Terminal
2. Copy and Paste this (one line at a time):
defaults write com.apple.Finder AppleShowAllFiles FALSE
If you are still having trouble after this, please let me know.