By my understanding the last version of LabVIEW that could be used for development of WinCE was 2013.
quote from Sam : "
I'll be honest, I didn't think NI supported PDA devices any more...given that Pocket PC & Windows CE is pretty much dead in the water these days in favour of Windows Embedded 7, Windows RT, Android and iOS (i.e. smartphones & tablets).
Newer versions (I've just looked at LV 2013) have the Touch Panel Module - but that only supports certain devices running Windows Embedded Standard 7.
"
Thus it might be possible that you problem is right there because labview in embedded system does not support. I cannot find more evidence to your specific problem. Sorry.