Have you tried to remove the parts of code (in the S19 file) that you won't be programing because of protected flash sector?
We could use this test to narrow the problem.
Deep debugg, we need to know if you are not erasing an important part of the bootloader code (in the MCU). Sometimes if you define sections with pragma instruction there are calls to ansii libraries that are stored outside the section we want.
How did you exactly ported the application to Win CE?
Are you trying to load the same application that used to work in Win XP? If this is the case maybe the problem is in the changes when porting to a different Win version.
Try to share a little more information so we can figure out the problem.