I know it isn't a direct answer to your question, but here is something you can try.
Go get Gary Johnson's latest book (3rd edition of Power Programming). In it, he dicusses embedding LabVIEW on a PC104. With his instructions, you may be able to figure out how to download LabVIEW code onto Windows CE. Otherwise, if you loaded Linux instead of CE, you can be sure to get your applications downloaded.
These are the latest news for NI LabVIEW development in Windows CE, certainly our R&D department is seeking for succesful solutions in the Windows CE environment so we are waiting for a future solution in this area.
Good luck!
Nestor Sanchez Applications Engineer National Instruments