CPU, Sys, and Sys2 all work properly.
Sys1 and Sys3 don't provide RPM readings, provide less than full power (although can't be sure how much, as they don't give RPM readings), and are not controllable (changing settings on these headers through EasyTune does nothing.)
All five fan headers on these motherboards are supposed to be controllable, but only CPU, Sys, and Sys2 are functioning.
After troubleshooting it is definitely just the two headers I'm asking about; it isn't the fans, or cables, or anything else. I can plug any of my fans into the CPU, Sys, or Sys2 and they all work just fine.
I'm looking for users of the Sniper board to comment on whether they have gotten Sys1 or Sys3 to function properly on their motherboards.