Default Copy speeds Fast on AOSPA, Slow on Stock?

Does anyone know what causes slow speeds when sending files to the phone?

I flashed back to stock because I never really gave stock a chance, when I got the phone I right away flashes AOSPA.

Now that I am on stock, I am transfering my DCIM folder from my computer (running Ubuntu) to my phone, I am lucky to get 2 mbps transfer rate.

When I was running AOSPA, I was getting at least 30 mbps if not more.

Is there any way to increase the speeds up a bit? I am using the USB 3.0 port on my laptop because that's where the real speeds are at for me

Thanks for all your help!