Since you're running OS3.9 setpatch should already be at the top of your startup sequence - I've just checked the version of scsi.device on mine, and it's coming up as 119.16, but then I use the "SKIPROMUPDATES scsi.device" option with setpatch.
40.12 is probably the version from setpatch - since it has already run once (at startup), running it again from the command line will not install any additional patches.
If you want to see what setpatch is patching at startup remove the QUIET switch from after setpatch in the startup sequence - the resulting output is slow enough (even on 060) that you will see the summary of what has been patched at the end of the spiel.
btw - I assume it is a pcmcia lan card?
