I *think* you're saying that you had a tray icon control but when you used it to show your application the skin was not displayed properly? If that is the case you might be able to fix it by trying the following one step at a time until the problem goes away:
1. Add a TsSkinProvider to your app main form if you haven't already.
2. Comment out everything in your form Create/Destroy/Show/Close/Activate/Deactivate events and see if the problem persists.
3. Change the events on the TrayIcon control to Hide/Show your form rather than performing some animation event.
4. In your FormShow event, reinitialize the skin manager. Try just setting the skin eg SkinManager.Skin := 'WEB (internal)'.
5. Download the Jedi VCL library and use their tray icon.
Good luck.