[rootlinux]

I don't use HTC backup so I don't know what all it backs up but if it backs up the registry then that registry may be the problem.
Stock registries do not have all the settings a custom rom has and the ones it does have will probably cause problems with a custom rom.
Then again it maybe files it replaces over this rom.
HTC backup was not designed for winmo 6.5.
I am pretty sure it will work but I would not run a stock backup over a custom rom.

That is probably an issue to research on HTC's web site.
Someone else may know a better answer than that.