I know its not my computer
And that computer is...? Sorry, such comments are useless if you don't provide exact specs. Of course your computer is part of the equation, be that hardware-accelerated playback or the underlying data rates for the footage I/O. The rest is equally useless since you have not provided exact comp and render settings. As a start, refer to this:
quad core AMD Phenom II 965
ATI raedon HD 5770
200G Western Digital hard drive
DDR3 8GB Ram clocked at 666.6MHz
Idk if anything else is necessary
The video file you encoded as lossless would be naturally be laggy (as the link Mylenium provided explains). A single hard drive can't serve up the data rate quickly enough.
However, (as the link also explains), if you pop that lossless file into the Adobe Media Encoder and choose a nice deliverable preset (the YouTube presets should work nicely), everything should be fine.
If not, what is your exact version number of AE? You said "CS6", but what's the full version number? 11.0.4?
After being encoded with the YouTube 29.97 1080p Preset it was still laggy and out of sync so yes im running Adobe After Effects 11.0.4
Can you share an example of this lagging/out of sync-ness?
I can reupload the youtube preset version but they play the exact same both files
I'll take a stab at this....
Get rid of all the compressed audio in your AE comp -- mp3, ac3, etc. -- and replace them with wav or aiff files. AE doesn't like compressed audio.