Sometimes that happens. I've noticed two causes...
1. You have declearations at the top of the css file. Something like the following. For some reason, this interferes with the ctrl-click link which is a know issue in Calibre.
@charset "utf-8";
@namespace h "http://www.w3.org/1999/xhtml";
2. If you run the CheckBook and EpubCheck functions, there will be errors. One of those errors is breaking the ctrl-click link. Once the errors are fixed, it will work again.
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