Strangely enough, this program was originally designed to get people w/o PhDs interested in research as a career. In reality however, most people who are interested in doing research as a career already have a PhD so most people who do the Research Track are MD/PhD. On my interview trail last year (and I only interviewed at places w/ the Research Track), I met a grand total of 1 person who didn't have a PhD and he was only kind of interested in the program. So, if you don't have a PhD, you may actually stand out in the minds of PDs. That said, you should have a really good reason for wanting to do the program (and a guaranteed fellowship spot shouldn't be the reason...that's the residency version of doing an MD/PhD for the free med school tuition).
As for the program itself. Gfunk is pretty much on the mark except that your post-doc time is 3 years instead of 2. Basically, you swap an IM clinical year for 2 research years. In a perfect world, fellowships are supposed to have ~50% of their time for research. In other words, a Hem-Onc fellowship (which is the one I know best) is supposed to be 6 mos clinical solid onc, 6 mos clinical malignant hem, 6 mos clinical benign hem and 18 mos research. By doing a research track in H/O (or other 3 year fellowship), you only do those 18 clinical months, do 2 years of IM prior and then do 3 years of research (90% protected time).
So the overall time investment (in spite of the short-track moniker that the program gets) is slightly longer than if you did a straight residency/fellowship track (6-12 mos, depending on the fellowship). The upside is that if you want an academic job when you're done, you're more or less guaranteed a junior faculty position in most programs.
As for the boards, you can sit for IM with the rest of your entering residency class (PGY-4 year). You can sit for specialty boards when you're finished with the program.
What do you miss in these programs? The chance to chill in your PGY-3 year. Although research track folks have the same requirements for board certification as other IM residents, they have to fulfill them in the first 2 years. This means 20 months of "direct patient care" rotations. In general this means wards, unit and ambulatory months. Apparently it can also mean IM specialty consult months but those cush Derm and Neuro consult months you were looking forward to may not count. So you squeeze the important parts of a 3 year residency into 2 years and don't get to relax as much as you might otherwise in your PGY2/3 years. That said, for many of us who have done the MD/PhD thing, we're ready to finally get a freakin' job already so speeding things up a little bit is kind of enticing.
Hopefully this answered some questions you had. PM me if you have more.
BE (now PE)