Configuration of the team mode is fairly straightforward, so I doubt that you are doing anything wrong in the team configuration. I do not know enough about the protocols used between your server and the NAS to make a specific recomendation. I also cannot tell exactly where things are slowing down. There might be something going on at the switch side or inside the system where the two adapters are teamed. The two adapters are connected into the computer differently, one using PCI and one using PCIexpress. There might be some bottleneck inside the system as a result of teaming these two adapter types.
You might want to check out the performance tuning discussion and suggestions at http://www.intel.com/support/network/sb/CS-025829.htm.
Another thing is to try some of the other teaming modes. Check to see if setting the team mode to static link aggregation mode works. Or you could try a teaming mode that is not dependent on switch groups such as Adapter Load Balancing. See if any of these modes give you the performance you are looking for.
Another possibility is trying a dual-port adapter in the PCIexpress slot and teaming the two ports. That would eliminate any bottlenecks caused by the system or by using adapters with different features. Of course the downside is you would only have partial redundancy on the ports compared to complely separate adapters. Or if you have another empty PCIexpress slot, you could use two single-port adapters.
You can also read more about the different teaming modes at http://www.intel.com/support/network/sb/cs-009747.htm. See the related links at the bottom of the page for some other resources.
I hope some of my comments are helpful to you. I am looking forward to hearing about what solution you use.