Exactly as the message says, you have policy-NAT commands in your configuration, and PDM does not currently support them. Because of this PDM goes into limited functionality mode where all you can use it for is monitoring.
The Release Notes for PDM v3.0 state this specifically (http://www.cisco.com/univercd/cc/td/doc/product/iaabu/pix/pdm/v_30/rel_nts/pdmrn302.htm#wp94255).
At this time there is nothing you can do about it, other than removing the policy-NAT statements from your configuration. PDM does not always support the very latest commands, it usually runs a version or so behind. Policy-NAt was only introduced into the PIX in 6.3(2), so the next release of PDM should support it.
