I have been using chkrootkit for over a year and I suspect it is prone to false positives. On the last one I could not find why it was saying 'last root user not logged in or deleted' (or something like that). Since I could not track down the source of the problem I gave chkrootkit the benefit of the doubt and re-installed which took over a day since the server configuration was quite complicated.
However, I made the decision to discontinue the use of chkrootkit and now use rkhunter which you can download from
http://www.rkhunter.org/ . chkrootkit might be alright but I got tired of re-installing what I *strongly suspected* were perfectly fine non-comprimised servers.
In any case, get rkhunter and run the scan. I run it as a cron job nightly like this.
/usr/local/bin/rkhunter -c --cronjob --skip-keypress > <some file>
Probably the commands --cronjob and --skip-keypress are redundant but hey!
Of course, to run it as a cronjob you must also do the appropriate crontab stuff.