I'm not familiar with this program, but have you tried restarting the dock?
If you haven't this, is how you do it: Go to: Applications: Utilities: Terminal
Open it you will see a screen with a prompt with something like:
Last login: Thu May 13 19:25:09 on ttyp1
Welcome to Darwin!
[Your-Computer:~] usr%
Type the command 'top' (without quotes) and press enter, you will see a lot of text. Drag out the window to make sure you see all the entries.
You will see a PID, COMMAND, %CPU, TIME and etc. columns.
Take note of the PID number. Close this terminal and when it asks whether you really want to terminate you can safely click yes.
Now open a new shell: Terminal file menu: new shell.
The same message will be waiting for you as before. Now type:
Kill PID
PID is the number you took note of before.
Your command will look like kill 756
Press enter, the dock should go away, before relaunching with hopefully, your new settings.