Could a codec issue be my problem?

Hi Guys, something has occurred, seemingly overnight, and I am trying to troubleshoot the cause. My workflow sees me render AVI from AE and then convert the AVI to mp4 or whatever in the AME. The size of my AVI files usally mean a render in AME takes 2 or less minutes. I have a grunty system so I can play the AVI without hassle. Last night I noticed the render time in AME was much slower than it should be, I know the render times of these comps and it was considerably slower. My system resources were not the problem. Today when I try to play the AVI in QT, the playback is choppy with second increments being skipped. Again this is happening when less than 8% of my system resources are being used. I have never before not been able to play the AVI smoothly. All of my drivers are updated.
My OS is Windows 8.1. CPU is i7 3820, 64G of RAM, Nvidia GTX560, SSD drives for programs, assets and source files etc all distributed onto different hard drives. I am working with AE CS6 (cloud version) and it is up to date.
I have been researching the internet and see people speaking about uninstalling codec packs and re-installing to fix choppy playback. I'm not sure whether this is something I should do. Apart from that I am at a loss as to what might have suddenly caused this. Any suggestions for where else to look would be greatly appreciated.
Thanks
Mandy

Hi Rick, from AE it was the default "Best Settings" 1280 x 720, Audio on AVI and in AME the YouTube preset. I doubt the render settings have anything to do with it - reason being, AVI movies that were rendered previous to this issue and have been watched many times without issue, are now choppy when watched.
As for what has changed, well I asked myself the same. I changed my keyboard and mouse to wireless. Also I deleted all my fonts and from another computer with the same OS, I re-installed the default set.
It may not have anything to do with the Adobe suite and more to do with my OS but I thought I'd ask both here and over at Microsoft and see what suggestions might be offered. I guess worst case I will look to do a clean install but I want to exhaust easier avenues first.

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Could a codec issue be my problem?

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