What version of InDesign? It's not happening to me in InDesign CS6.
Two possibilities I can think of. Your method of trashing preferences isn't working. Try this method:
Second possibility: You've installed a third-party extension that this interfering with your InDesign keyboard shortcuts.
Abberant behavior in Keyboard Shortcuts can also mean that you are using a custom set or that you are using a custom set that was copied from an earlier version.