Seems that Ive discovered the same issue on my crafted lvl. 31 BXR-55. Got both enhanced perks and the enhanced intrinsic but the weapon is still no Masterwork. Maybe it depends on in which order you crafted the enchanced stuff, because if I remember correctly, I crafted the enhanced intrinsic on my Ragnhild at the end and it became a Masterwork. Dont know what cause the bug but I hope that Bungie will fix it in the near future [b]:-)[/b]
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Had encountered the exact same issue with the missing masterwork frame on the weapon earlier this evening on the same weapon. Hope Bungie will fix this soon too :)