If after performing the normal configuration and diagnostics you do not have or cannot use all of the ports on the Intel® PRO/1000 MT Quad Port Server Adapter card, you most likely have run into a known BIOS limitation.
This limitation is described on Intel®'s website at: http://support.intel.com/support/network/adapter/1000mtquad/sb/CS-009534.htm#knownissues under
Shared Interrupt Limitation. Intel® states the following:
"In some systems, the BIOS and OS assign the same interrupt number to two or more different ports on the Intel PRO/1000 MT Quad Port Server Adapter. If this occurs, these ports do not function properly. In this case, reassign the system resources so that each port of the adapter has its own unique interrupt number or disable one of the ports sharing the same interrupt number."
It is recommended that you read about the known issues in the above reference to assist you in avoiding the described problem.
Note: You will need to make these changes to your systems BIOS. The BIOS in some systems may not allow you to make these changes.