Windows dual boot specifically likes to corrupt it or has in the past. I've periodically checked in on
nix desktops over the last 20 years. Red Hat, Centos, Fedora, Suse, SLED, Mandrake, Slackware, Gentoo, Gentoo on a SGI O2, Debian, Ubuntu, Mint, Open BSD, FreeBSD, DSL, Puppy Linux, Solaris, Open Solaris, IRIX, Arch, OsX, the venerable hackintosh, and last off the top of my head BeOS which was somewhat POSIX compatible if not a nix.
So, the crap that sucked in 1998 is the same stuff that sucks today. Inconsistent clipboards, graphic driver/X11 support, multi monitor support and debugging/positioning issues, poorly documented or improperly configured out of the box network management tools, firewall, etc. tools. Boot loader failures, and (more significantly recovery). Inconsistencies between Qt, Gnome, Kde apps, graphic sub system freezes. Pulse or whatever sound system of the month suddenly failing one day. DVD playback, MDADM failures, Drive partitioning and resizing difficulties, File system corruption (is it disk based sure but windows is less prone to it on the older file system types, ZFS, XFS, etc. are nicer).
If you want to compile an application, run a server, etc. nix beats out windows any day. If you want to be able to install this great new linux thing you heard about on your existing computer, surf the web, manage your photo collection, hook up your scanner to copy in those old pictures of your kids, setup your Nvidia card and play some games on Steam, find and install the latest or a specific version of an app with out hitting the command line and typing things out like madison, then Linux is not the desktop for you.
edit and don't get me started on high end xeon and intel chip support/speed step handling, or version upgrades running successfully.