I found a somewhat crude work around. I have tested it and it is working so far. 
I use 1-8 in global mapping for my apps and then 9 for stickies. Then I created some apple scripts. 
1-8 uses the same basic apple script: 
if stickies is open then open my app if it isn't open then pass thru 1-8 depending on the number entered and it also closes stickies then in the harmony software under favorite channels my app channels are 91-98 so first the mac mini opens stickies then opens my app. if stickies isn't open it passes through the number so I can use it for my favorite channels in eyetv.

Not sure if that makes any sense or not. I know you can create a file with an apple script so instead of opening stickies you could create a file and then look for the file. if the file exists then open the app, if not pass thru the number. and then delete the file once the app is open.

I still lose the use of 9 but atleast I do have most of my numbers available for favorite channels.