I had a similar issue, with my Galaxy S4 and Pioneer 4100NEX. Replacing my USB cable with a high quality short one (thewirecutter.com/reviews/best-micro-usb-cable) fixed the issue for me. I purchased both the 1 foot and 3 foot version of the Monoprice cable in that article. Both work excellently.
Recently though I had a weird issue where the home screen (and only the home screen) above the "dock" would look like it was launching, then go to black, then launch, then go to black (the dock itself remained on the screen at all times). All the other screens were fine (map, phone media) and all functions worked (music streaming, map routing and rerouting, voice texting, etc.). I tried a bunch of things to get it to work ... I tried disconnecting and reconnecting my cable, restarting my phone, restarting the stereo by shutting off the car completely and then restarting it, and forgetting the stereo in my phone's bluetooth settings and then re-pairing. Nothing worked. I then tried uninstalling the android auto app, forgetting the car within the app, clearing the app data and cache. Still no go.
What finally did work was going into the bluetooth settings on the deck itself and deleting my phone from it's memory, then removing it from my phone's bluetooth list. Then I re-paired again and everything worked.
Just a head's up if anyone else has that weird problem. It's 2 days since I reset it and the problem hasn't resurfaced.