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Yes same issue with File Vault, that have experience similar issues on older Macs with File Vault enabled in regards to login slowness, odd avatars or having to login twice, etc. It's one of the down sides of using File Vault.

However with the new MBP's it now asks to enable it during the setup process so imagine most people have it enabled compared to the past now, which is why the issue is getting more attention.
 
Actually we were just making sure it's a software problem instead of a graphic card fail

I don't think that follows at all. If a software configuration can cause the GPU or display to do this, something is wrong with the way the hardware is wired up.
 
I spoke to apple regarding this. They said it seems to be hardware. Attached is a image of when it happens.
 

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