Ok. So I actually identified a bug. From SAS "... [the] PROC QLIM developer ... confirmed that the behavior you are observing, that when Z1 = 1, Z2 = ., the procedure treats the missing value for Z2 as a different level, is indeed a defect in the procedure. The developer also confirmed that this defect has been fixed in the next release, SAS 9.4TS1M6. "
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