I can't see how it's affecting the proximity sensor or shortcutd. I can't reproduce any issues either on Thumb or Non-thumb. Are you certain you have checked other software isn't causing this? Have you only just installed FlopSwap or have you just upgraded? Which version FlopSwap? What other applications do you have? What settings do you have in shortcutd? Have you setup your swap partitions on the uSD card correctly? What settings are set in FlopSwap? What happens if you press Show Current and Check Status?