Can't see clip keyframes in timeline

Hi Caleb
Here's my 2 cents worth and I hope it helps.
I have often found that the Dynamic link process can be a bit 'naughty'. I'm assuming you are initiating dynamic link inside the timeline inside Premiere by right clicking on the clip and choosing >edit in After Effects, or similar method.
You could try this little hack to see if it's a dynamic link problem. After AE has opened with the relevant footage and composition, immediately go back into PP and choose >Undo to revert your clip to its original state. This will break the dynamic link, but the AE file will not be affected. Then try adding keyframes and see if problem is still happening.
And, of course, as mentioned by others, one of the other culprits may be the drop-frame format of your footage. This time, before sending to AE, try choosing >Interpret footage inside premiere to conform to whole frames (ie. 60 fps instead of 59.xxx).
Worth a try 🙂

What happens when you use the Jump to Next, and Jump to Previous keyframe buttons (the arrows) located on the Timeline to the far left of each property with an active stopwatch.

There is nothing in your screenshots that tell us anything about what may be causing the problem because they are cropped so much. Also please embed the screenshots using the toolbar.

To reveal keyframes press the U key, then press k or j to jump to the next available keyframe. The CTI will park on a keyframe. We have no way to tell if you have zoomed in on the timeline so that you can't see the keyframes. 

This could easily be user error instead of a display problem. Please don't crop your screenshots and show us all the modified properties in the layers you are having problems with by pressing the U key twice.

Start by checking whether you actually have applied the latest update. Several of those keyframe-related bugs were fixed in those updates.

Mylenium