Autobolt has worked pretty well for me. Do you possibly have bolt selection codes assigned? have had instances where bolt set is assigned a selection code, and applied to valves. The bolt set is then deleted from the spec, but the selection code remains assigned to the valve.

So autobolt is unable to place the bolt then as it cant find the selection code.

However saving the model and reopening to find components missing, can relate to autocad save issues.