Just to be clear on this, and after looking at the OpenGL code, there is no bug that should cause this to happen in the VBA-M code. As long as this is working on other video cards on Linux, it is definitely a card-specific issue.
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ATI cards have notoriously poor Linux support. So even if that card works for VBA-M in Windows, there's no guarantee it will work in Linux. No video card manufacturer has perfect Linux support, but You're going to have a much better experience in Linux if you have an Nvidia card (or even an Intel card, though you won't get the same kind of performance as ATI or Nvidia).
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This is because the ATI drivers on Linux are pretty poor. Both ATI and Nvidia refuse to release the specs for most of their cards because they fear that if they do so, the other company will steal their trade secrets. That means that it has been up to the Linux community to reverse-engineer the cards and write their own drivers. Since it's mostly volunteers doing this, some cards have solid Linux drivers and others don't. Currently the reality is that Nvidia cards tend to have better Linux drivers than ATI cards.