Read here click here which explains what the dirty bit is in the boot sector.
If the dirty bit keeps getting set in normal useage, then either you've got a faulty hard drive or a software issue of some kind.
I would recommend you set SMART to Enabled in the BIOS, and run some SMART checking software (ActiveSMART has a free trial I think). This will give you some indication of whether your drives are getting too many errors (which will slow your system down).
You should also do a Disk Cleanup, and run up-to-date AV and Anti-Spyware software, in case either of these are corrupting your boot sectors.