Hello I am the author of the project "HERE":http://www.smartqmid.com/phpBB3/viewtopic.php?f=10&t=2441&sid=c720aa25ed5e77203973b7f71ca465d0 and I would like to help.
After reading your first post it reminded me of the week long attempt I made at compiling Qt for Windows Mobile then for Wince 6. Through my struggles I managed to accomplish both and have began a tutorial (still needs some work) to help others in this struggle. You can find that "HERE":http://www.smartqmid.com/phpBB3/viewtopic.php?f=21&t=2433
Anyhow, enough introduction. I personally think your issue is similar to what Milot spoke of.
Your configuration for Qt compilation may work fine when using the application on wince 5. But the compiled libraries may contain some dependencies that are not located on your windows ce 6 device. Keep in mind that not all builds of windows ce are created equally. Each "rom" is built using platform builder, and depending on what options were provided by OEM/rom developer, your Qt libraries may be incompatible.
That's where Qt configuration variables come into play. Some versions of wince don't provide cursor function and other options, so don't include cursor functionality in the compilation or whatever is not available in YOUR specific build. You need to determine what is available to your wince 6 environment and build a custom configured Qt environment to fit it.I don't know how to check specifically on the device what features are available; I had to build 8 times before I got one working.
Check out my tutorial and try the application I am working on (links above) and see if that helps/runs for you.
If you would post more about your device/environment: like screen pixel count,amount of available memory, device model/ manufacturer, I might be able to help more.