I don't know if this is the same problem you're having, but I had an issue for a while that if I changed one of the dock shortcuts, no matter which one I tried to change, it always ended up changing the first one. So basically once my dock was set-up I had to keep it that way.
What I figured out was that if memory usage was too high (especially if I had a live wallpaper running) launcher pro wasn't holding on to my selection throughout the process of changing it so it reverted back to the first shortcut. If I turned my live wallpaper and other memory suckers off, then I could change the shortcuts just fine.
I don't know if this is the problem you're having, but I hope it helps.
OP:every time i change the tray icons to another icon than stock it works for a bit but when i use the cell it disappears...any reason why ?? am i the only person with this issue ?
This is a known issue. It happens with the Dialer and the App Drawer icons. Long press on the icon, select Change Shortcut, and select Blank. Then go back in and long press again, select Change Shortcut, select Applications, select Dialer and then select your custom icon. Repeat the steps for the App Drawer if using a custom icon for it. I was having this same issue and my icons have been perfect ever since performing the steps above. Hope this helps!
You are welcome. You should be set. I figured this little work around out almost a week ago (found it, I take no credit) and I have not had them change back once when initially they were changing back almost hourly.