i might be mistaking but I remember having the same issue a while back and it was that u have to accept the one u received from checky like complete the quest or something. if u buy it from the shop it wont work . try that and hope it work =D
if u check correctly ur potential stats on weapon do apply twice so u don't lose anything ur actualy saving money cubing a second item. I might be mistaking but I remember checking that a long time ago pretty sure the wep count for potential is double like if u get 13% atk u actualy get 26% 40% boss u get 80 and so on.