I dont understand why the timeline indicator sometimes splits. Like the yellow bit at the top ends up somewhere different to the red line. Can someone please explain this to me. Thanks
What version of AE? There are several elements to the timeline. Work Area, background cached render (blue line), ram render (green line), time navigator indicator. Yellow and red indicators, if I remember right, are from an older version of AE and indicate the frames that are stored in ram.
There is a lot of information on the AE timeline here. Check it out if you are new to AE.
It's just a driver issue. If you're using CC try going to the display preferences and checking the Hardware Accelerate Composition, layer and Footage panels.
One more thing. You don't have to scale your uploaded images way down. We can not really see anything if you scale them to 400 pixels. Just leave them screen size.
I re-read your posts more carefully and was misunderstanding your problem.
When you do a Ram the Yellow CTI at the top of the timeline does not move. When you stop a ram preview the red line should snap to the current position of the CTI. If you play with the space bar the CTI will snap to the frame where you pressed the space bar the second time.
I had thought that you were getting separation while scrubbing or dragging. What you are seeing is normal behavior. There is no need to fix anything.