Was this once working as you expected, and then something changed? How are you using the two ports? Are they bonded/teamed?
What OS were you running on your PC when you tested? How did you measure the throughput on the ports?
If this is a hardware issue with the adapter, I doubt that there is anything you can do to bring it back. If your PC is running Windows, you could try running the diagnostics on the adapter to compare each of the ports to see if anything shows up there.
This worked before, I could measure 200Mbit from my WAN on both ports.
I have not changed anything.
I use both ports, the card is in a pfsense router, one port for WAN, and one for LAN.
I have tested both Windows 7 x64 and pfsense, same results on both machines.
I am measuring via a swedish testsite, Port 1 measures 100Mbit, port 2 200Mbit on the same connection, same cable.
Though modem, card an PC indicates 1Gbit connection, port 1 can only bring 100MBit.
The diagnostic says both ports are ok.
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I believe the next step is to replace the adapter. If you are the original purchaser of a retail adapter, the limited lifetime warranty applies. If you contact Intel customer support, they will help you.
If your adapter is not covered by the warranty, I would consider buying a newer adapter. The Ethernet controllers have gone through a few generations since your adapter was developed. Check out this comparison between the Intel® PRO/1000 PT Dual Port Server Adapter and the newer Intel® Ethernet Server Adapter I350-T2. Of course you will have to check out compatibility with your router if you change adapters.