should I let dskchk run?

I installed IE9 today, and when my laptop turned back on from restarting, a screen appeared that said my C: disk, file type NTSF, needed to be checked for inconsistencies. I also got some sort of code (TI106040W0F), and was given 10 seconds to skip the check. I let it run automatically, and it started to rapidly scroll text on the screen. I couldn't make out most of it, but every other line said that it was deleting a file from my C: Windows folder. I shut off my laptop and turned it back on, and was greeted with the same screen. This time I skipped the check; I was brought to my desktop, everything works normally, and IE9 installed properly. But, every time I turn on my laptop, I get the same prompt to skip the check or let it run. I had never seen or even heard of this before I installed IE9. All things considered, should I let the check run? I really don't want to do any damage to my laptop.

I let it run and didn't have any problems. It also didn't prompt me about the check again when I restarted after the check (some people have had that happen). Thanks for the help, and for the fast response. I'll make sure to come back here if I ever need help with windows again.