Apple just released a press release stating:
We are continually trying to make the App Store even better. We have listened to our developers and taken much of their feedback to heart. Based on their input, today we are making some important changes to our iOS Developer Program license in sections 3.3.1, 3.3.2 and 3.3.9 to relax some restrictions we put in place earlier this year. In particular, we are relaxing all restrictions on the development tools used to create iOS apps, as long as the resulting apps do not download any code. This should give developers the flexibility they want, while preserving the security we need.
This might have to do with the ban on applications that have been developed using Flash, which resulted in an investigation by the FTC.
Update: Developers have to login to the iPhone Developer Program Portal to review and accept the new agreement.
Remco van den Elzen