I've had some trouble with my Wisbar Advance 2 skins failing to load the softkey bar section of the Today screen, and the Lakeridge site has a FAQ item on this issue that might pertain to your problem.
The Windows Mobile operating system allows only so much room for DLLs (system libraries) to be loaded due to the 64MB memory constraints. WisBar Advance uses a DLL to enable the skinning engine. If this DLL cannot be loaded, menubar skinning will not work. There are a few remedies for this:
* Reduce the number of DLLs being loaded by turning off Today screen items
* Reduce the number of programs running by closing them or setting them not to restart automatically (for those that have the option)
* Increase WisBar's boot delay (go to WisBar's settings > Times/Delays)
Rather than alter my program or Today-screen items, I tried the latter suggestion (changing from 0 to 5) and haven't had a problem since, but it's only been about a week.
I also had trouble with PocketMusic's Today plug-in, which like your experience would not show on the screen about half the time. I don't know if this is related to the WA2 problem. I emailed their tech support who said they were aware of the problem and working on it, but I just disabled the plug-in, which I can live without.