Ive installed the patch, and installed the assets2.pk3 file
to my installation path/base directory.

when I run
./jk2ded +set dedicated 1 +exec server.cfg

I get a segmentation fault.

(Its actually in the section "InitGame:" apparently where its parsing all the game data..)

So I tried running the 1.02c dedicated server binary...and it seg faults too. If I remove the assets2.pk3 file, it runs fine, actually, both 1.02c and 1.03 run fine if the assets2.pk3 file isnt present. Ive recopied the assets2.pk3 file several times to be sure I have a good file there, but it makes no difference. The permissions on all the assets*.pk3 files are set the same so thats not it either. Any body got any ideas?
Im even only using the default server.cfg that comes with the binaries (which has always worked fine in the past).

Just on an off chance, did you make sure to set the ftp mode to binary? I've made the mistake of leaving it as ascii a couple of times and it made a nice mess.

Actually, I copied directly across my network from an xp box to my linux machine. Ive got samba running with a public folder set up on my linux machine. Maybe the file is getting corrupted somehow there, although I can open the pk3 file in my linux ZIP program, so I wouldnt think that would be it...maybe I'll burn it to a CD and try passing it that way instead of through samba.

MD5SUM :

88369ad9f959cbe64a6d948f08305d20 assets2.pk3

This file works for me. Oh, and make sure the file is readable by the user executing the jk2ded binary.