Hardware Joy-Cons no longer working wirelessly?

[Captain Library]

Hi folks

I've got a Switch running 5.1.0 (installed via ChoiDujourNX) with ReiNX v1.6, and an unhacked Switch on stock 6.0.0.
Joy-Cons work fine in handheld mode on the hacked Switch, but when removed from the rail immediately turn off and do not attempt to connect wirelessly with the console. Pressing buttons does not connect the Joy-Cons. Change Grip/Order does not connect the Joy-Cons. The lights will blink and then stop.
I've tested this with 4 pairs of Joy-Cons.
I have not modified the Joy-Cons except putting new shells on one pair.
One pair of Joy-Cons has the firmware update from the unhacked Switch.
Joy-Cons work fine on the unhacked Switch.
The hacked Switch is not in airplane mode.

Any ideas what might be causing this?