Check if the user code measures PCLK properly. If it doesn't, then the baud rate calculation will be wrong. Since one of the symptoms that has been seen is that the RX light on the FT232 doodad flickers, but no characters appear in putty, it is possible that the baud rate isn't what we think it is.
Consider also calculating the baud rate registers and stuffing them manually. If this works, then it's the PCLK stuff that is broken.
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