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...press Ctrl + Alt + F1 at the beginning of the boot process?
Then I see a few lines of text, and after 5 seconds my GUI loads. If I let it boot the normal way, it takes more than 2 minutes. Is there something wrong with this way of booting? I haven't experienced any problems I know of yet.
It shouldn't make any difference, ctl-f1 should just be showing messages that come up during the boot process. I'm not sure why it would be faster, but if it is going so much faster it shouldn't hurt anything.
Are you using the ext2 filesystem? If you are you should let it check it every once in a while. If you're using reiserfs or ext3 it shouldn't need to be checked unless the computer lost power for some reason. Also, ext2 is usually set set to check itself every 30 mounts or so, that may be why you saw that message.
You are correct. Does this mean I will be having no problem if I bypass the file system check?
Sure. I don't think it's bypassing the file system check that is speeding it up. The check is run every 30th time you boot, not every time. So it wasn't running anyway.
Ctrl-Alt-F1 isn't really bypassing anything. It is dutifully launching a new virtual terminal, complete with X, just like you asked it to. The boot process is probably still going on in the background.