Ok, one thing I would do is open a ticket with the help desk and have them give it a once over for the trojan warning. The other thing I would do is ask those users having problems accessing your site if they are on the Road Runner network. I'm on Road Runner and I was having all kinds of issues accessing sites that I knew were up because I could access them from work where we have AT&T. I have switched my DNS to use OpenDNS instead of Road Runner's DNS servers and haven't had an issue since.