FastLED automatically turns interrupts off on AVR chips when needed, and back on afterwards. The problem is that the Neopixels are so slow that interrupts are turned off for so long that it really trends to screw with pretty much any kind of interrupt-based communication at all.
We sort of all take it as axiomatic at this point that you can't have these three things all at once: an AVR microcontroller, WS2811/WS2812 Neopixel leds, and normally-functioning interrupt handlers.
Moving to APA102 is one popular solution. Another is having a separate microcontroller handle the interrupt code, and have it communicate with the LED MCU via a non-interrupt-based (serial?) connection.