We are encoutering a problem with Intel proset 15.8.76 (last Hitachi Data System supplied version).
We have several 802.3AD Dynamic Link Aggregation teams, with two X520 server adapters or two 82576 server adapters.
When a network connection is disabled, then enabled from Windows (2008 R2 SP1) or on the switch (port down then up), the link does not come up. On the switch side (Cisco Nexus 7000/2000) the port cannot be brought up again (it goes done immediately). After a server reboot all links are up again.
I would expect the link to come back up when the port comes back up. I looked through some old bug records. Although I did not find an exact match, I saw some bug fixes that could be related. I recommend testing with the latest Intel software as a next step. I would say that you have a fair chance that the issue will be resolved by upgrading.