Not that it really matters anymore, but we are using ixgbevf 2.16.1 and ixgbe 3.23.2.1 on Ubuntu 14.10 (kernel 3.16.0-36-generic).
If I look at the ixgbe code, specifically in ixgbe_srio.c for function ixgbe_ndo_set_vf_bw(), I can see that it tests for 10 Gbps mode before allowing me to set the rate limit. We've instrumented the code, i.e. added printfs, to see that this is actually the place where setting the rate limit fails.
Now that we have the adapter in 10 Gbps mode, setting the rate limit works. Previously we only had a CAT5 cable, which is why the adapter was only operating in 1Gbps mode.