You should be able to fix this very easily
Just place the configuration controls 2 or 3 pixels lower, and also inc the labels size a bit (multiline labels a bit more).
Windows CE based devices may don't have all fonts installed. This problem seems to be related to this issue. If the os is falling back to another font (which may be larger), the controls may be to small.
I have had this problems in my own applications, too
But I have another suggestion
I believe that some users may can't get your application working. In germany (don't know its the same in other countries) all prepaid cards with internet enabled are limited to use only the ports 53 (dns), 80 (http) and maybe 443 (https). all other traffic is denied, including ntp.
Whats about to place a script on a web server and sync to this time? Because of this, it should work for all users (should only be added as an option, because of the additional delay)