Im not sure if navigation panel is the correct name, but.

When selecting album, video, and the video starts playing then there is a menu below the video where you can change volume, pause and so on.

I have figured out that i can move the playing video up/down and left/right
<param group="General" name="Image X" type="integer" comment="Adjusts the horizontal position (in pixels) of the image." value="0"/>
<param group="General" name="Image Y" type="integer" comment="Adjusts the vertical position (in pixels) of the image." value="-5"/>

But how can i alter the cordinates of the menu below the playing video?

Because it looks pretty lame when the video and the "navigation panel" is not aligned.

You need to play with the 'Main panel xxxx' settings.

I have tried playing with
<param group="Main" name="Main Panel Y" type="integer" comment="Adjusts the vertical position (in pixels) of the main panel." value="255"/>

Tried changing it from -100 -> 100

Example:
<param group="Main" name="Main Panel Y" type="integer" comment="Adjusts the vertical position (in pixels) of the main panel." value="50"/>
img232.imageshack.us/img232/3372/exampleol2.jpg

This setting changes, nearly everything but the "navigation panel", im really lost.

Another idea?

The flash is a mystery for us too. We build the bridge for the standalone component from www.slooz.com. Seems like the main pannel doesn't include the video panel... Could be hard-coded in flash; don't know anything else.
Could it be that your gallery is to big for the provided space? This sometimes generates strange layout issues.

Video panel is a separate panel and can't be manipulated at this point.