I've just reported the same problem to your support team. This is really penalyzing for large companies using Exchange servers since synchronisation of iphones can't be automatically deployed anymore !
I personnaly don't think this is a bug in Apple's IOS 4.0.2 since it worked perfectly for me on my Ipod Touch 3G before installing Files Lite. Furthermore, a collegue running the same IOS on the same ipod without Files Lite gets no problem. And the biggest problem of all is that uninstalling Files Lite doesn't restore Safari's default behavior (which is to automatically open configuration profiles).
If you have a workaround, please think of me too !