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.
Good luck, and let us know.