Global clock, virtual pins & incremental compilation

I last tried those scripts long ago. A clock-related limitation I ran into then still hasn't been enhanced. You might be seeing another limitation rather than a bug (the scripts are provided as a convenience without the intention of them doing everything for you). If you confirm that the scripts created a virtual-pin assignment on an input that the scripts should have known is a clock, then I suggest filing a mySupport service request regardless of whether it is an intended limitation or a bug.

The critical warning probably isn't hurting anything if the timing is good when you compile the complete design at the end. I think I'd still do what the Quartus handbook says and not have a virtual-pin setting for any clock input to the lower-level partition being compiled in a separate Quartus project.