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I am new to using Ubuntu and VB, so if this isn't the right place to post this question, let me know.

Using a Windows 8 host and installing Ubuntu 16.04 LTS in VB, I cannot use seamless mode without the application's window's becoming invisible. The preview in VB shows that the OS has booted. Ubuntu notifications even appear as if they're on my Windows desktop, so I know the application is running.

I have 3D acceleration enabled and inserted guest additions. Below I have a screen capture of what the problem looks like. You can see the Ubuntu toolbar at the bottom as if it's on my Windows desktop.

Invisible windows

Full-screen mode works fine, but not seamless.

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Not sure if this was the direct cause of this issue, but I had just updated to VB 5.1.2 and that seemed to be causing some issues. They have a separate download for Guest Additions for Linux guests that might have solved this issue. Instead, I downloaded a slightly older version and that worked for me.

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