You might be correct, though I thought this kind of stuff died years ago. Anyway, If you have "emergency" boot floppies, try them out. First, the one for Linux, then the one for Windows. They should (in theory) work regardless of any MBR problems (because they exist only in case your MBR is screwed).
If both work, then you need to use your windows boot floppy to boot windows, and search through control panel or the compaq setup stuff (compaq was a BS company back in 1993, and even now I get shivers when I see that name
), then turn off stuff like virus checking the MBR (which might be a bios setting, by the way--in fact likely), and such in that group of settings. Otherwise, each time you try to boot, the computer will try to wipe out anything written by Lilo or Grub (whichever bootloader you happen to use).
Basically, your computer is seeing (whether it's the Bios or other Compaq software is up for debate) Linux as a virus, because in order to boot linux, you have to modify the MBR, which is a staple of virus writers. (Well, it used to be. Nowadays, virus writers are more interested in "owning" your computer, in other words, using it for their own needs.)
Oh, and are you sure you lost everything on your Windows drive? The only way that would happen is if you accidently (and you'd have to hit okay a couple times without reading the red warnings) overwrote your windows partitions. Windows, as well as Linux, may seem to "disappear" on some installs, but that's only an illusion. Unless you agree to overwrite a partition, there is no way for an install to erase data on another partition. To the computer, they are completely different items, and might as well be on different sides of the planet.
