Unfortunately, this is the only solution they give to this problem. My first search turned up the information that running "chkdsk /r" assumes "chkdsk /p", so I figured that you could just bypass the /p step by running the step that does both. Upon further searching, I found that it is crucial that you run /p before you run /r. Why? I have no clue. Try running "chkdsk /p" again followed by "chkdsk /r".
As for the "troubles" that occur while starting up, it's hard to say. What startup problems are you having?