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Have you tried the latest ixgbe driver, version 3.11.33? You can get it at http://downloadcenter.intel.com/Detail_Desc.aspx?&DwnldID=14687 or from SourceForge.
If you are using the latest driver and still not getting the packets passed up to the application, then the issue might be the way the multicast filter is configured. If the latest driver does not help, get a dump of the Ethernet registers using Ethregs available at http://sourceforge.net/projects/e1000/files/Ethregs%20-%20Register%20Dump%20Tool/1.16.0/.
Mark, thank you for your quick reply! We installed the ixgbe-3.11.33.tar.gz driver and the issue persisted. However your mention of the multicast filter reminded us about it and we ran: sudo sysctl net.ipv4.conf.all.rp_filter=0
Which has fixed the problem for us! So thank you again for your fast response, we've resolved this issue.