The most likely cause: the frame rate of your comp and the time display units don't match, e.g. it's a 59.94 comp, bu the time display is set for 30 Drop Frame.
Try rebooting your machine. See if that helps.
Also, are you using CC 2014 or CC 2015? Actually, what is the full version of AE down to the last decimal?
Also, what OS?
I've rebooted and it hasnt helped
Mac OS X 10.9.5
AE CC 2015 13.5.1
It seems an awful lot like frame rate mismatches somewhere like Dave says. So I would double-check everything.
Clear all caches too.
If that doesn't help, try opening that project in CC 2014. CC 2015 has had a number of oddities with it and this will help determine if it's an issue in your project or just an issue with CC 2015.
If you don't have CC 2014, you can easily get it: How to Find and Install Previous Version of Adobe Apps in CC 2015
Take a close look at your CTI. It's exactly on the frame marker. What you are seeing is the shutter phase. You set that in the Advanced Tab of composition settings. This is only visible if you have motion blur enabled. Check out these screen shots. This is actually an important indicator of how motion blur is going to work especially when you are trying to match motion blur on footage with motion blur on graphics. The width of the grey line shows the shutter angle, the position shows you the phase or when the shutter opens in relation to the time.
180º and -90º is the default and that looks like what you are seeing.
180º at 0º gives you this display.
720º at -90º looks like this. Notice that the blur starts half way before the next frame but extends over 2 full frames.
It's a little hard to explain without a video tutorial but what you want to do with Shutter Angle and Shutter Phase is match the movement of your graphics with the motion blur in the footage. Say someone is swinging a baseball bat. At the first frame where there is motion blur you have to adjust your shutter phase and angle so that your graphic has the same blur on it's first frame of movement and on the last. This is where phase comes in. The amount of blur is matched with the Shutter Angle. This can be different for each shot. That's what is going on here. There is nothing wrong with your comp settings and this is not a bug. It has nothing to do with the 3D layer problems.
Here's the view with motion blur turned off: