This might or might not be related to fixes to Glamour bug.
What happens:
When equipping soldiers from craft, sometimes some items that ARE present on the base, are NOT visible. It appears to plague such things as grenades, medical supplies, flares. It appears random. Here is a save (from Xcom files), where you can check for yourself (compare items available from craft soldier equipment menu to items available if you use 'inventory' function in the main 'Soldiers' menu; as far as I understand the Apoc style equipping, and how it worked up to now, was that availability was the same). The missing item becomes available if you put it on craft, but then the availability is limited to the amount you put on craft, like in the classic equip method. It appears like the game was using the old and new method randomly for random items.
Please let me know if bug description is confusing, it's hard to spell out clearly, at least for me.