MUX SEL input "was determined to be a clock"?!?

That generally means it's driving a clock port of a register. Obviously from the description that sounds incorrect. A few thoughts:

- Look in the Fitter Report -> Resource Section -> Control Signals, sort on Usage and look at everything that is a Clock. This is not a TimeQuest report, but a physical report of everything that drives the .clk pin of a register. Just see if something stands out.

- In TQ, put a create_clock assignment on the signal it says, then do report_timing to that clock. See what shows up.