Problem is all the installed Operating Systems must share the disks and as at start the bios only scan the first one, there must be a so called "partition table" in the very beginning of this disk. This partition table is located in the Master Boot Record (MBR) side by side with the boot loader.
Any misuse of the MBR by any of the OS's leads to problems. When trying to install any system, yes answer at a question like "automatic partitioning ?" is likely to give problems... This is specially true with windows, especially with custom windows installation made by special makes PC's (when no true "windows" cd is included). But it's also true with new "smart" (not so smart !) Linux installation programs given with most recent distributions.