We have paid developer account for iphone development and we have 2 iphones one jail broken and other one non jail broken. We have registered both phones for development and
I personally do development/testing on jailbroken devices (I find that it is nice for profiling/debugging with all the UNIX tools available, as well as testing out code for checking for tampered plist files ;-) ) as well as non jailbroken devices.
I have not had any problems specifically with jailbroken devices, as they behave exactly like stock standard firmwares..
Have you: