sorry for the late reply
"Which Nessus version are you using? And what portscanners are in use?"
3.0.6, ive tried a few different methods and port scanners.  Ill have to
check what I have enabled now, been tweaking them to see what gives me
better results.

"transient services on high ports could do this. firewall manipulation could
as well."
A lot of the high port things are more then likely this, im looking into
firewall changes as well.

"Could you be more specific in the ports you are seeing? On one hand you
say that the system admins know about these ports and they've been open
for years, but then you also mention that you can't connect to them with
nmap or telnet.

I'd try to work backwards from the systems themselves by running a netstat
command on them."

They range, a lot of high ports which as noted before could be some
transient services.  Though some are things like a few telnet, http, ftp.
 Quite a lot more, but I get alerted on these perimeter ports.  I may have
misrepresented my problem a little, nessus does see these ports one day
(some have banner info, I know these are not false positives) but others
nessus will alert and the next day these ports wont be seen when I follow
up.  I've contacted the system admins on a few of these and they tell me
these services are not listening or have been listening for years.
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