Strange flickering

After playing for a while (1hr-2) i begin to see my desktop flicker past FFXIV and i can see it like "closing and opening" on the taskbar (like i see it vanish from the taskbar then immediately reappear but the game is unaffected by this). the longer i play the more often it does it. I am baffled as to what is causing this. I DID just install a brand new CPU so unsure if that has anything to do with this. it's just weird, it like, flickers up my desktop for a split second then goes away, its kinda annoying and ONLY does it with FFXIV, i can use itunes/firefox/HWMonitor/task manager/skype/etc just fine :/ (EDIT: I noticed it doesnt do this if it isnt the active window, also its not just the desktop but whatever is behind the game at the time, like a browser for ex)

Information I can provide:

CPU: Intel 3770k (previously had an old dual core amd, bought a new motherboard with the intel core too.)
GPU: geforce gtx 650 series (with current drivers)
RAM: 8GB DDR3
OS: WIN 7 (Fresh install, had to in order to wipe old AMD drivers that conflicted with the new intel ones)

Game running temperatures for CPU and GPU: CPU did not exceed 62C(143F), GPU did not exceed 61C (141F)

CPU load during heavy load areas: 20% at most

FPS on average: 30-60 depending on congestion

EDIT: i switched to FS and back to windowed and now it isnt doing it...shrug :/