Installing to internal storage was correct, as most of these CE 5.0 devices automatically wipe RAM clean on reboot, so they'd have been deleted had they been installed in \Windows. As for registry settings, what you can do is use a registry editor to export the entire registry to a file in the internal storage folder, and then re-import it after you reboot. A bit of a hassle, no doubt, but better than reinstalling everything every time.
I suspect, though, that it's the opposite problem: that the device in fact has a persistent registry that it reverts back to on reboot
(unless there's a device-specific way to save changes to the persistent registry
). You can check this theory by opening a registry editor and selecting
(not expanding
) HKEY_CURRENT_USER and/or HKEY_LOCAL_MACHINE to see if there's a key called "RegPersisted" and checking its value
(1 if enabled, 0 if disabled
).