I had a similar problem when building nessus 2.0.1 on SuSE 8.0.

I had to try many different things and it finally worked after I installed gtk-devel and glib-devel AND installed without the GUI. Check this link >> http://www.nessus.org/doc/faq.html#Q.COMPILING.SUSE

So:
Install the nessus "packages" in the order specified >> http://www.nessus.org/install.html
Use ./configure --disable-gtk when installing the nessus package
Use NessusWX to access your server

According to this answer (http://msgs.securepoint.com/cgi-bin/get/nessus-0303/149.html), there might be a problem with xdevel. I haven't check this before, but I will when I install 2.0.2

Cheers,

Marc

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