See attached screenshot.
The cog menu z-index (1000) is lower than that of the user tour step dialogue (10402).
We need to fettle some z-indexes.
It also looks like the tour z-index math is wrong:

$flexitour-base-zindex: 1040;

z-index: #{$flexitour-base-zindex} + 2;

This results in a z-index of 10402, instead of 1042.