The programs are very similar but I found that Trackmasters is a somewhat "tighter" program. By that I mean that after hearing the classroom lectures a couple of times with SCDA, very little additional new information would be introduced. As I mentioned in another thread, the SCDA classroom instructor takes his powerpoint presentation from the Skip Barber book "Going Faster." Having read that book, I learned very little from classes after the first couple of track events.
I also found that it is more difficult to "move up" in class with Trackmasters than SCDA. Although your ego might want to tell you that you should jump from novice through advanced quickly, I have felt that drivers with Trackmasters seem more experienced in each level and that probably is because you do not get signed off to go solo as quickly as it seems drivers do with SCDA.
With that being said, I did start off with SCDA and did not do Trackmasters until after about 8 events with SCDA. I feel that I received competent instruction with SCDA and have no problems with recommending them. Trackmasters, on the other hand, would have a slight edge for my recommendation in terms of getting more practice in recognizing flags and potential dangers on the track because they actually have on-track drills where they will throw a red flag to see how the drivers react and then critique everyone on how they handled themselves in that situation. I was amazed at the number of drivers with similar experience as me who made mistakes when these flag drills were performed.
No matter who you start with or what track you go on, just remember to listen to your instructor and don't drive beyond your abilities. There are no prizes or trophies so just make sure you are technically proficient and speed will come later.