Controller not available at boot

[mscreations]

Hello,

I'm having an issue that isn't Retropie specific exactly, but since that's the distribution I'm using I'm hoping someone here might have an idea.

I have my Raspberry Pi 3B+ installed in a NESPi case. If I have my controller's dongle plugged into the front, the controller does not work after startup until I unplug and replug the dongle. I am using the PDP Afterglow PS3 controller.

Running lsusb right after boot through ssh yields:

Bus 001 Device 004: ID 046d:c52b Logitech, Inc. Unifying Receiver
Bus 001 Device 005: ID 05e3:0608 Genesys Logic, Inc. Hub
Bus 001 Device 006: ID 0424:7800 Standard Microsystems Corp.
Bus 001 Device 003: ID 0424:2514 Standard Microsystems Corp. USB 2.0 Hub
Bus 001 Device 002: ID 0424:2514 Standard Microsystems Corp. USB 2.0 Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

After unplugging and replugging the dongle, I DO get an extra entry:

Bus 001 Device 007: ID 0e6f:1314 Logic3

I'm not sure what else to do to try to figure out why the dongle does not appear to initialize when the Pi starts up. I've tried multiple raspberry pis (RPi 2B and 2B+) as well as multiple distributions (Retropie 4.3 on older pis, Retropie 4.3.15 on the new 3B+, Raspbian Jessie and Stretch).

This problem only occurs if I plug the dongle into the NESPi's built-in USB hub. If I plug it directly into the Pi, it works everytime without any issues.