Ive been working on a tutorial project and I experienced this ... "lag" thing when I was recording in Soundbooth. When soundbooth would generate a waveform timeline image, it was WAY off from what the audio actually was. I have to delete it from inside the soundbooth program, go into where the files are created and re-import/re-open them into Soundbooth. Then it'd be accurate for that file from then on. Closing Soundbooth all-together allowed 2-3 accurate recordings before the problem came up again. This was pretty frustrating, but workable. But then the problem started happening in after effects. When I change properties of keyframes, the timeline and even the layer outline in the composition reflected changes accurately, but the images themselves, the layers I guess, would remain unchanged until I grab the layer with the mouse from within the composition with my mouse and move it even a pixel.
I have scanned for viruses, malware, junk-ware, and adware. As far as I can tell, my system is clean. It's almost like the memory, CPU, or GPU is getting overworked. All of these things I'm extremely unfamiliar with.
Has anyone heard of or experienced similar problems?
We can't know. You've written a lot, but said nothing. You have not provided any useful exact info like system details, program versions and so on.
Adobe's apps are the bugs, scanning for viruses, malware, junk-ware and adware won't solve the problems. Only Adobe can fix their software, and they are in no hurry to do that.
Best alternative approach is to find alternative software and correct your incorrect assumption that Adobe releases polished, professional grade, production ready software. They don't.