Heh yeah the good old days of Vatsim, needing to fire up several different programs, all in the right order, then cross your fingers it worked. These days voice, weather, MTL and metars are all in one program - Squawkbox.
Are you running SB3 on the same PC as MSFS? If not you may need to copy the 'vip' folder from your FS9 directory to the PC running SB3.
If it's on the same PC, look in :\Program Files\Microsoft Games\Flight Simulator 9\Aircraft\ for the vip folder. this is what renders the planes. If that's not there perhaps reinstall SB3.
If that's all in order then look to a firewall/router issue. Are any ports blocked that could stop data being received by your PC? If you use Windows firewall try turning it off. That blocks incoming but lets outgoing data out.
Maybe also take a look at the SB forums at
http://squawkbox.ca/forum/index.phpGood luck!