I would download and install Lavasoft Ad-aware 6 and Spybot (both are free for single user). Run both those apps on a regular basis to clean your server of any spyware and adware. Then download a popup blocker. I like the builtin blocker that comes with the google toolbar.
Most likely you're receiving netbios adverts that use the messenger service - if your server has a public IP address and isn't firewalled very well then this is how the ads could be arriving.
Disable the messenger service......
I came across another scanning tool recently. Bazooka Spyware Scanner. It scans much like Ad-Aware and the others but instead of just clicking a button to remove the bugs it gives you an explanation of the bug, where it came from, who to contact for possible uninstall information and detailed instructions for manual removal. You can find it at Kephyr.com. Check it out and I hope it helps.
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