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For a long time there has been a bug in the activation done by the initial pvscan (which scans all devs to initialize the lvmetad cache.) It was attempting to activate all VGs, even those that were not complete. lvmetad tells pvscan when a VG is complete, and pvscan needs to use this information to decide which VGs to activate. When there are problems that prevent lvmetad from being used (e.g. lvmetad is disabled or not running), pvscan activation cannot use lvmetad to determine when a VG is complete, so it now checks if devices are present for all PVs in the VG before activating. (The recent commit "pvscan: avoid redundant activation" could make this bug more apparent because redundant activations can cover up the effect of activating an incomplete VG and missing some LV activations.)