Hi smerrett79
Building on what PaulRB said and what you have tried, Adafruit recommend a 1,000uF capacitor across the neopixel power connections. Also, a 330 to 470 Ohm resistor between the Arduino data output pin and the input to the first neopixel, at the neopixel end of the connection.
But maybe before that, what happens if you disconnect the neopixels (leaving the code in your program)? If there were a clash between the neopixel library and the Manchester code library, this ought to show up even if no neopixels are attached.
I know that the neopixel library disables interrupts when it sends the data to the neopixels.
Regards
Ray