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so they are protected cells. that can be the problem. my 501b laser doesnt like protected cells at all. wont work with them period. try buying some unprotected 16340 for cheap
What turns me away from it being the protected cells is that he has to wait before it will come back on. The protection circuit should turn off after the load is gone so it would flicker almost. At least in my experience. I wouldn't run two different batteries.
posted the 16340s i use in my laser. most unprotected 16340s are ultrafire but those have been good to me