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Some users were reporting a high FAIL rate on gene and transcripts quantification. This has been resolved according to a battery of tests using real and simulated data. The root cause was that in conditions with substantial overdispersion across replicates, the FPKM variance-covariance matrices produced by the Cuffdiff model were not always positive-definite. Cuffdiff was detecting this, and marking those genes as having unreliable confidence intervals. Prior to 2.0.0, the model contained a heuristic approximation of the covariances between assigned fragment counts (which are necessary for calculating the variance on each gene's expression level), and this approximation was producing poorly conditioned matrices.  

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