HJS,
It is true that CAD packages for designing flex are specialized with different sets of design rules than PCBs with notable differences in smooth arcs in traces and teardrops for pads. The reason for this is the mechanical differences in the flex design to account for bending. There isn't really any CAD package that solves all design issues related to the many variables that can impact a flex circuit design, but there are some good packages that specialize in the mechanical design aspects of the circuit.
On the other hand, that does not mean you are completely locked out from using your PCB layout package to create a flex design. You should be able to use the CAD package you are most comfortable with, but work with a flex manufacturer to review/fix your design for violations of flex design rules and best practices. To not go through the appropriate design rule checks would be potential trouble.
A quick check of Mentor website seems to indicate that they have a Flex Technology module for their circuit design packages that utilize some flex design rules. We don't have any experience with it but it is another possible option to consider.
Vitreous Humor
"Eye can see clearly now..."