MacOS – Open application several times in OS X

This seems to be a problem with permissions in the bundle itself. Usually the execution flag doesn't get carried over from the DMG image.

Try, for the sake of curiosity to set the execution flag like this:

chmod +x /Applications/RubyMine.app/Contents/MacOS/<name of the app>

Note: replace <name of the app> with the name of the app (it will probably be "rubymine", but I don't have that app to confirm the exact name of the binary.

If you're in doubt, right click on RubyMine.app, do a "Show Package Contents" and navigate to Contents/MacOS/ folder and see what's in there. Perform the above command (chmod +x) on that file and try again.

I think it should be:

chmod +x /Applications/RubyMine.app/Contents/MacOS/rubymine

update: I've downloaded RubyMine and the above command will work, however, for what is worth, I've got to say that mine had the execution flag so I didn't have any problem with it. Have you checked?

Sure this problem applies for both your drives? Could be that one drive affect the other thru your USB controller. Try to disconnect one of them and see it it gets better. If it doesent, swap them to see. If it gets better while one of them is disconnected I would limit the problem to be a faulty drive.

You could also try to check if some processes are accessing your drive. Have you checked torrent or so aren't loading to the drive(s)?

Alternatively you could turn off the option for spinning down your hard drives when possible in your settings panel for power.