Shortcuts Work Intermittently

I am fond of windows shortcuts, and I've put together a number of them (CTRL-ALT-_) to streamline my work.What happens sometimes is that they stop working - why is that? I have 6 folders shortcut'ed, for example, and if I close all folders, then any shortcut will work once. If a folder that has a shortcut is open, then no other folder shortcut will work until that folder is closed.Some shortcuts work always never a problem. Others work sometimes, not other times. I have my shortcuts folder in my start/programs folder. I read once where they had to be in one of two places, and one of those was the programs folder.

I did find that if Reflection (Unix terminal screen app) was running, and a portion of the screen was highlighted with the mouse as if you were going to copy it to clipboard, that it would stop some shortcuts from running. It's a mystery to me, and I've wondered about it for so long, I thought I would finally ask the forum if they had any clues.