Group policy prevents application from accessing registry

I developed an application in the past which ran in a workgroup environment where all our users had the potential to access the registry. I am moving everybody onto a domain and implementing group policies.

I would like to allow my application access to the registry but not the user.

Any ideas would be greatly appreciated (Directors whish to see their expensive server hardware put to use, staff can't work without my app, the standard traditional rock and hard place).