I have this problem too but it doesn't seem to be a user rights issue because my NDMP user is in the administrators group with admin role which has cli.*. It's not a problem accessing the filer with SSH because I use PuTTy+SSH from the same Windows box to manage my filers. And it's not an issue with my NDMP user since I just re-set that up in DFM and copy & pasted the NDMP password (plus it works once I enabled the DFM option mentioned in my next paragraph).
As suggested by Netapp Management Console (NMC), I set the dfm option to user all interfaces. After doing that, my job in NMC still did an event "retrieving preferred interfaces" and it succeeds and finds my main VIF that I want it to use, along with my e0M management interface. Luckily, it appears to be using the main VIF like I want, because I have NDMPD logging enabled and it makes connections on the VIF and doesn't make any connection on the e0M. The job succeeds, so I guess this works fine for me.
Could this be a bug? Anyone out there able to set the preferred NDMP interface and still use NMC for SnapVault backups without setting DFM to user all interfaces for NDMP?