>So sysdef and kmtune "should" return the same values correct?
No because the timestamps ARE different:
kmtune requires /stand/system to be present so it uses it, if the timestamp is different with /stand/vmunix you could have a missmatch : someone updated the kernel but hasnt updated the system file, or someone has edited and updated /stand/system and hasnt rebuilt the kernel...

sysdef reads the values from the current kernel.

>what about why sysdef does not return values for some params whil kmtune does? sysdef | grep shmmax returns nothing
Ah well thats one of many params sysdef will not show...

Now 'sysdef' is deprecated, and kmtune is the correct tool to use with 11.11
and post 11.23 you should be using kcweb as in future sysdef should be removed...