I've used several versions of the 2.4
I've used inbuilt and standalone
I don't have the winCE version in front of me, but I do believe there are 2 different versions between the 2 devices.
800x480
All units have always has the files in the root. I havn't tried putting in a subfolder, such as "MobileNavigator", which could be part of the problem
I have always deleted the save folder.Possible I have the wrong settings in the sys.txt, but the same sys.txt has worked for me in many previous versions.
I have 2.4 running on my wife's 4 year old android tablet. If she ever brings it home for me to try it, I might get somewhere.