74HC595N in series error
If you had it working and it has changed, I would suggest trying a few changes to track down the issue. The schematic seems OK so assuming that all connections are sound, I would look towards proving the code. Maybe try a simple pure Arduino sketch designed for the 74HC595N and see if the results are the same. If not, the culprit is almost certainly Johnny Five.

Perhaps try this sketch which should work with your schematic (remap the I/O though to your 2,3,4 configuration). If the problem persists, throughly examine your connections because there is very little else which would prevent it from working - especially given that it did work a few days ago. Also, have you got another Leonardo to test with?

Finally, the schematic for the Arduino-only example shows a cap on the latch line - presumably for debouncing - which is missing from your schematic. I don't think you've damaged your registers but I wouldn't rule it out.