Yes, there are at least a few other formal 5-year MD/MS programs that I know about. Here's my alphabetical list of formal 5-year MD/MS programs. If anyone knows of any others that I should add, hit the comment button, and I'll be happy to add the links. Keep in mind also that a lot of med schools offer informal options to take a fifth year and get an MS. So even if you go to a medical school that doesn't have a formal MD/MS program, you still may be able to get the MS.
1. Albert Einstein College of Medicine (AECOM) Clinical Research Training Program (CRTP). Gives an MD/MS in clinical research. Medical students apply during their third year and do research in their fourth year.
2. Cleveland Clinic Lerner College of Medicine (CCLCM) at Case Western Reserve University (CWRU). Options include an MD/MS in clinical research or one of several basic science MS degrees, or a 5-year MD with Distinction in Biomedical Research. Premedical students apply to the program separately from the main Case program. The last three years are flexible, and the research year can be done during the third or fourth years (or some mixture). There are several combined masters programs available through Case for both CCLCM and UP students. UP students will probably need to take a fifth year to complete most of these masters programs.
3. Harvard-MIT's Health Sciences and Technology (HST) Program. Offers an MD/MS or an MD/PhD. Premedical students apply to the program separately from the main Harvard program. It seems to be geared toward people who want to do engineering type of research.
4. UMDNJ-Robert Wood Johnson Medical School MD/MS in Biomedical Informatics. UMDNJ-RWJMS medical students begin the MS after their second year. Note that this program takes 5.5 years to complete. There is also an MD/MS in Jurisprudence, which seems to be geared toward people who are interested in health care regulation and policy. The MD/MSJ can be finished in five years.
5. University of Pittsburgh's Clinical Scientist Training Program (CSTP). Offers a clinical MD/MS or MD with Certificate in Clinical Research. U Pitt also offer a basic science MS option for people who want to do research in basic sciences. Premedical students apply to the program while applying to U Pitt. Students do research in their fourth year.