When right clicking a nesting pen with any item they disappear from my inventory, and only reappear when another inventory is opened. If the item is placeable, it places for a split second then disappears, but will still reappear when another inventory is opened.

Little confused on this one. Are you talk I about an item in your hand disappearing? Anyways thats a client server desync. ill check it, but havent seen that happen yet.

yes it leaves my hand and my inventory, its like im using the item, but im not because it re-appears after I access another inventory

I Saw this happen the other day. not sure whats causing it. but it now needs more research