Do you have a feel for whether this is DNS related or HTTP related? I assume
from the above that its more likely to be HTTP related.
Am I correct in assuming that you run an http proxy on your server? I do not
have SBS Premium, so I do not know what comes with it, but I would assume the
proxy/gateway on your server is the likely culpret.
However, a few other suggestions:
1. You referred to a speedtest showing your speeds lower than they were. If
you can tolerate complaints from your users (or do it out of hours) it would
be interesting to know what the figures are if you plug a pc in directly to
your touer/modem and then re-run the tests. The rational being that if a pc
on the network is generating a lot of internet traffic then that could be
using up much of your bandwidth and that would cause you to see lower
results than you might expect.
2. Since you have ISA (I do not), I think this allows you to see where your
network traffic is going. If so then can you see whether anything in
significant is standing out as using a lot of bandwidth?
3. I assume you have checked the logs on the server for any issues and not
found anything significant?
4. I had an issue a number of years back now where our network seemed to be
slowing down (but interestingly seemed fine for a few minutes after a reboot
of the server), tracked it down eventually to masses of spam being sent out
via our server (NDR spam). So its worth having a quick look at your exchange
queues and if you have large amounts of emails awaiting delivery then that
might be the cause.
Of the above all the ones which relate to something eating your bandwidth
would also affect FTP, SMTP etc, but I suspect that people are less likely
to notice if these are slow.
Hope this is useful, even if to rule out some things.