Every now and then when you boot up your Ubuntu machine (and this probably applies to most distros) fsck will be run to check your filesystem. Depending how fast you machine is and how large the filesystem is, this may take a while.
A script called AutoFsck allows this test to be done when you shutdown your system, this way you don't have to wait for it looking at a black screen.
Also, there is a simple command line utility that can tell you when the next fsck will be run for your filesystems: showfsck. Just install it with apt-get and run it as root. The output is a bit strange, shows UUIDs, but at least you know how close the next fsck it.
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