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Most visual settings for can be edited within the Advanced Options Dialogs "Menu" tab.  To open this window, click on the "Options" button on the right of the menu, and choose "Advanced Options" from the menu that drops down.  If necessary, click on the "Menu" tab.

Menu Title
This changes the title displayed at the top of the menu.

Minimum (and Maximum) Number of Application Buttons to Show: can dynamically resize itself to show a particular number of icons in the left panel before displaying a scrollbar.  Thus the size of the menu can be changed based on the number of applications installed, and the resolution of the monitor displaying the menu.  Modifying the minimum and maximum number of applications buttons to show will change how this behavior works.  If you want to fix the menu at a particular size, you can set both values to the same number.

Behavior on unknown computer: can behave differently on computers that you have not designated as "Known" (or trusted) computers.  There are several options:
      Display Owner info and quit - This will display the owner information you have entered into, then exit.  If you misplace your usb drive, hopefully, an honest person will read this information and return the drive to you.
      Run menu from unencrypted drive- If you are using TrueCrypt, you can use this option to not mount the TrueCrypt partition and instead load your applications and documents from the unencrypted partition.  This Option will allow you to install different applications (or the same applications with different profiles) to be run on untrusted computers.  For example, you might install FireFox with a profile that saves no history and sets cookies only for the current session.
      Mount TrueCrypt Volume as usual - If you are using TrueCrypt, this option makes behave the same way on all computers, whether they are known or not.
      Mount TrueCrypt Volume as Read Only - If you are using TrueCrypt, this option mounts the TrueCrypt volume as read only, so that you can run security applications such as malware scanners without risking that malware can infect the TrueCrypt portion of your drive.  Be aware that unless you are using a Portable Drive with a physical read only switch, the USB drive's host partition could be infected.
      Mount Alternate TrueCrypt Volume - This allows you to specify an alternate TrueCrypt volume to mount on unknown computers.
      Display Owner Info and Run Menu from Unencrypted Drive - This will display the owner information you have entered into, then (if you are using TrueCrypt) will not mount the TrueCrypt partition and instead load your applications and documents from the unencrypted partition.

Owner Info
You can enter up to three lines of owner information (address, phone number, etc) that can be displayed on unknown computers (see above).

Keep Tray Icon to the left
This option will attempt to keep the icon to the left of the system tray, so it is easy to locate.  Some applications conflict with this option and cause the icon to disappear, but generally this is not the case.  Note that this does not apply to Vista or Windows 7, which have their own system for managing system tray order- you can simply drag the icon to the left on those systems.

Accelerate Menu by loading apps from File
If you are running from a slow USB drive, you can allow to save the contents of your drive to a file, so that the initial loading of the menu will be faster.  In most cases, the amount of time saved by selecting this option is minimal.

Autoscroll Menus
If you find it annoying to click on the scroll bars to scroll through your applications, you can click on this option, and when the mouse moves over the scroll bar, your applications will automatically scroll.

Show Personal Picture
If you do not want to load or display a personal picture on the upper right corner of the menu, you can hide the image by unchecking this box.

Include Batch Files on Menu normally scans for ".exe" files to create shortcuts for the menu.  If you'd also like to pickup and display batch files with the ".bat" extension, choose this option.

Known Computers
This is the list of known computers used by the "Behavior on unknown computers" described above.  You can add or remove computers from this list by clicking on the buttons on the right.