I am not sure there is anything you can do about the router. By the time the router sees the traffic the NAT'ing has been completed and their is no record of the NAT'ing except form the device doing the NAT'ing.
You could however put the ASA on 8.2 or higher code and have the ASA send the flows and then you would be able to see the internal addresses.
This is exactly what I had to do, however it appears that the Netflow traffic is not as accurate, there is data missing when looking at graphs, but I don't know if thats an ASA Netflow thing
Netflow was recently added to 8.2 code which is not that old, it's relatively new so maybe they are still working out the details.
I will have to go with another tool or something that uses Monitor Ports, Anyone have suggestions on tools that work in a scenario such as this?
I had a similar problem when I setup Netflow on my ASA's.
ASA's were sending back netflow data on incorrect interfaces. To fix this I discovered the ASA's, and then added all interfaces into the monitoring (EVEN the down interfaces!!)
Afterwards, all the Netflow data was shown.
This might be your problem as well