Isaac doesnt start with the D6???

[ChestnutGore13]

So I beat Isaac (Cathedral Boss) as ???/Blue Baby. It was an UNSEEDED run (I never use seeds bcs what's the point?), I got the D6 achievement which says that "Isaac now holds the D6", yet Isaac doesn't start with the D6! What's up with that? I tried quitting the game and restarting it but Isaac still doesn't have the D6! I am somewhat upset and disappointed because I've heard from a lot of youtubers that this item is very fun and makes the game much more enjoyable and I had to beat the whole game with ??? to unlock it, but I can't even use it...
Note: I only have TBOI: Rebirth, and I do not have have the DLC yet.

[Desticler]

Try verifying game cache. It's possible that there's an error in files that makes Isaac not start with D6, if this is the case verifying game cache should fix it. If not then I have no idea what the problem is.

[Nazemec]

A loose players.xml file in the game files can do that.
Go there (adapt to wherever you installed Steam):
C:\Program Files (x86)\Steam\steamapps\common\The Binding of Isaac Rebirth\resources
Delete everything except "packed".

[ChestnutGore13]

♥♥♥♥♥♥♥♥♥♥♥, I figured it out!
So what happened was I originally beat Mom, It Lives, and Isaac with ??? all for the first time on the same run (I got Brimstone and Tammy's Head lol). I got the D6 achievement on Steam but didn't get the "secret" in-game. As it turns out if you beat It Lives and Isaac for the first time on the same run, the game only registers It Lives on the little paper progression tracker (not sure if that's intentional or a bug), but the game legit didn't register that I beat Isaac, and so I had to bloody do it again, which I did and now I do have the D6 on Isaac.