[apl]

I managed to find a solution should anybody else try scripting with the key/value user data dictionary.

The following script fragment generates a list of shapes with the key/value pair of aURLkey and "Hello".

tell application "OmniGraffle Professional 5"
	set matchingShapes to shapes of canvas of front window whose value of user data item "aURLkey" is "Hello"
end tell

Hope it helps