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I had (and still have) a problem with Fifos and Quartus on some projects. On 3-4 projects that I currently maintain, there are a few fifos that have the same behaviour that you describe. The usedw signal is correct, but not the full and empty signals. The only workaround that I found was to delete all generated files, including the db and incremental_db folders, and compile the project from the beginning. Then the fifos work as expected.
You could try and see if you have the same results.
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Oh, dear!
I will try this. I have too many trouble with FIFOs. Just a moment ago, a SCFIFO has the full flag set but usedw all zero.
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