From your description it doesn't sounds like it matters if you go over fabric A vs B, it's which controller creates the LUN that seems to make the difference here.
The usual stuff to check is the active zoneset and make sure that both initiators (one for A and one for B) are allowed to hit the respective ports for the A and B controllers on the Netapp.
If the blades are supposed to boot from these luns then you can SSH to the UCSM address and after a reboot run the following to get a report from the option ROMs that should tell you more about what's wrong:
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==================== VIC FNIC driver does not support Virtual Volumes (
second level LUN ID ) An enhancement request has been created to track
this feature - CSCux64473 UPDATE - 12-14-2016 We made some traction on
the enhancement request - The Fix is in t...