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The R implementation of DESeq2 and DESeq2(R) fail to generate results in some special cases of input data that are handled differently in Partek's implementation of DESeq2. 

First, if two or more categorical factors are present in the model, there can be a situation when some combinations of factor levels have no observations. In Flow, one can see if that is the case by clicking "Cross tabulation" link after the factors have been selected:

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In all of the special cases, an informative warning is output in Flow log. 

Since there is limitation in DESeq2(R), we recommend to use DESeq2 task all the time.

References

Love MI, Huber W, and Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 2014;15(12): 550.

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