So i'll give both a go and see if either solution works.
Sometimes that suggestion from Bitmain does work because if the fan is not detected properly it would cause some issues but we do not know exactly without the kernel logs.
Why not, do what Bitmain suggested and run it for 30 minutes or 1hr and then copy the kernel logs and paste it here. So that we can analyze why you get 3TH/s.
I also want you to try flashing the unit through the SD card but the problem is I can't seem to find the s9 SE SD card image under TF cards it seems Bitmain removed it.
So maybe it would fix your issue if you still have contact with Bitmain try to request for SD card image for the s9 SE and then flash it back with the firmware available from Bitmain through the WebGUI.