The "We have the way out" campaign is a joint effort between the two companies to promote Unisys' ES7000 Enterprise Server, which can run a data centre version of Windows 2000.
The server/operating system combination is being promoted as an alternative to Unix-based server products.
On Monday, it was revealed that a Web site set up to promote the advertising campaign was running the FreeBSD operating system, a free version of Unix. Netcraft, a UK company that monitors the software and operating systems being used by Web sites, said that the site at www.wehavethewayout.com was running Apache server, another piece of open-source software.
Then, on Tuesday, the site disappeared. Attempts to access it bring up an "Error 404, file not found" message.
According to Netcraft data, the anti-Unix site was migrated on Tuesday from the FreeBSD operating system to Microsoft's Internet Information Services (IIS) 5.0 software on Windows 2000.
Neither company was able to comment on any connection between the switch and the disappearance of the site.
"I'm aware that there's a problem, but can't tell you any more than that at the moment," said Jill Pearcy, a spokeswoman for Unisys in the UK.