I know it's a very old Thread but i think any hint for 'is it a false positive or not' is welcome.
I had that same warning yesterday
[06:31:44] Warning: Hidden Processes found:
[06:31:44] Warning : sysinfo test skipped due to intermittent activity
I did run, ofc, chkrootkit and another run with rkhunter (CD Binary), looked through all etc etc. when i noticed that the machine was somehow slow. ell, long story short:
~/w2tmp # cat /proc/mdstat
Personalities : [raid1]
md3 : active raid1 sda4 sdb4
1847608639 blocks super 1.2 [2/2] [UU]
[===============>.....] check = 79.2% (1463721792/1847608639) finish=59.1min speed=108177K/sec
That's what caused the false positive in my case. I was able to reproduce the exact same warning on one other Debian 6 machine while the raid was rebuilding.