For some reason when I try to launch the bots using /bots or skillup it gives me 'unknown command' message
/graphics does the same thing. I am missing some files ?

Fresh install of nquake. Appreciate anyone's help on this....

After launching ezquake then try typing in console:
map dm6
Addbot
Skillup

Still gives you unknown command?

Doing it that way - running ezquake-gl direct works, but if I run the nquake shortcut and try those command it gives the 'unknown command'

I uninstalled nquake and re-installed and for some reason it didn't re-create the nquake shortcut on the desktop. Do you know where the default .exe for nquake is saved or why this is happening? I was pretty sure nquake was just a front end for ezquake , but it seems that running ezquake directly has different features.

Since it was a while ago i installed nQuake, i re-installed it now to replicate the problem. I didn't get any shortcut on the desktop, but i did get one in the start-menu called "Play QuakeWorld" that simply leads to /nQuake/ezquake-gl.exe and for me it was possible to add bots like in my previous example.

Perhaps it's only the Java based version that creates the shortcut . It seems a lot of the features are missing w/ Java option over downloadable . i,e bots etc. Makes total sense. Thanks for confirming the same results. Once I get my new box - I will test with fresh installs.