It looks like this is a symptom of a bug inadvertantly introduced in VX.2.1 by some other changes made to property handling. This has been addressed with the forthcoming VX.2.2 release.
You and I previously addressed a similar issue that is almost certainly related. The 2nd of 4 gates in a part had all of its pins marked invisible by default. In addition, the gates were repeatably generated out of order. Are you aware if the VX.2.2 release solves the general case?