I understand your frustration, but I cannot reproduce this problem on macOS. For example, Cmd+A always works, no matter how long or how hard I work on a running PixInsight instance, including very complex projects. The same is true for the rest of shortcuts. Currently I have two iMac computers at hand, one with OS X 10.10 and another one with 10.11, and keyboard shortcuts work on both.
Please provide a reproducible pattern to understand why this happens.