I'd be suspicious about the display blinking; I used to get that and it ended up being a faulty power source (no ground, in my case).
Skype issue might just be Skype configuration; they may have their own settings for which device to use, which tends to get out of sync with OS configuration.
also don't know if my mbp retina hardware or software, but sometimes my display blinks, it also happen with my old mbp (2010) but was not till updated to mountain lion, so maybe is a software issue too? (din't check it, will wait to read some feedback about the update)