I found this bug on windows 7 with HD 4000. Appears to come with HD 3000 too.
When the gl clear color contains 1 in any channel, the glBlitFramebuffer call seems to overwrite the MSAA buffer, and the next blit becomes black.
I created a small program (code included) to demonstrate it:
Tested with the following clear colors:
1, 1, 1, 1 -> BAD
1, 0, 0, 1 -> BAD
1, 0, 0, 0.98 -> GOOD
1, 1, 1, 0.98 -> GOOD
0.4, 0.58, 0.93, 1 -> GOOD
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