I am the Associate Dean for Graduate Admissions at Illinois Institute of Technology
and I can tell you that we, at least, don't get too concerned about transfers as long as the grades and GRE scores are to our standards. There are all sorts of reasons why a student transfers, particularly in these times when college expenses are getting so high.
The biggest problem facing a transfer student for graduate school applications is the fact that it is harder to get letters of recommendation form faculty who have known you for a long period of time and can convincingly speak to your strengths. The letters of recommendation are extremely important in differentiating applicants who have similar GPA and GRE statistics.