I am not sure this is the issue, but there is a problem with the latest gprof binaries. See, for example,
Subject: gprof time accumulation problem
Newsgroups: gmane.comp.gnu.mingw.user
Date: 2008-08-23 20:53:05 GMT
http://article.gmane.org/gmane.comp.gnu.mingw.user/27398and Danny Smith's response
Subject: Re: gprof time accumulation problem
Newsgroups: gmane.comp.gnu.mingw.user
Date: 2008-08-23 22:58:53 GMT
It sure would be nice if a new release was available.