Noise Isolation tips
That is the nature of these neopixel devices. They have no output inductance or capacitance on the PWM switching.  They generate a lot of EMI.  

With a PWM frequency of 1.2Khz,  the 1.2khz noise you are experiencing is expected.  

It would be best if the 5.5 switcher, 5v LDO, and LEDs had their own ground plane.

Follow the PCB layout and decoupling guidelines to reduce conducted EMI. This Vishay Engineering Note covers them well.

Insert an input filter on the 12V line in to the switcher.

This is the EMI filter TI recommends on the Vin on their TPS92511 LED driver to suppress conducted EMI. For frequency between  1.2khz and 2.4khz the values would be around 10µH and 68µF.