Yes, those are the three main possibilities. A fourth (but highly unlikely) possibility is that the small cohort tested was abnormal in some way that has not yet been discovered.
Could be that 12 weeks are not enough and longer treatment will do better, could be resistance (I assume they are analyzing virus pre and post treatment), could be that another agent is needed.
Longer durations are worth trying but personally I feel it won't make a difference with patients relapsing at 12-weeks after achieving a RVR. The trend appears to be set. Using a third agent seems like the best option with nulls but unfortunately drugs outside the nuke class aren't known to have strong resistance profiles.
A safe purine nucleotide (monotherapy/dual nuke) could possibly overcome the shortcomings of the GS-7977/Riba combination.