@MrStruders If by fresh install you mean using a new image, then no, since the new image will write everything from scratch. Can you run another update, also updating the OS and packages when prompted, of the RetroPie-Setup script ?
I'm having the same hiccups since updating to 4.4 (4.3.17 practically) but it could be a "nocebo" effect due to the hefty amount (45GB) of titles, box art and videos (unrelated to the RCA topic I made previously).
I'm pretty sure though that things were slightly faster before (3B with 4.3 instead of 3B+ with 4.4) and that "hang for 5 seconds" thing I'm too having didn't happen until 4.3.16/17. To put it in a sentence, navigation feels a bit more laggy and stiff than before.
However, I'm not having the second part of adm166's problem with images showing grey, etc which sounds like a VRAM issue.
@retrocraze you may try to set the resolution you want (smaller than your tv native resolution) in the config.txt file and, in your tv video aspect options menu, set "original" or something similar, depending on your tv brand.