[Zageron]

This is likely because Skype uses hardware acceleration properly, and flash does not. When Skype is "activated" your video card would turn itself into high power mode to run whatever was necessary for Skype, when the notification is over the video card returns to low power mode.

If you have an NVidia video card, you can find your standalone executable and register it into the profiles area in the NV Control Panel. Reduce the prerendered frame count to 1, and force high performance mode.

This may help, it may not. (If you use an Intel Embeded graphics system or an ATI card, I don't know how to force high performance modes. )