I see this is an older post, but I'm going to throw my two cents in. Hopefully I'm referencing similar to what you've experienced. I won't have my Renegade for a few more weeks, so I can't speak to the vehicle itself.
I have a 2013 Scion FR-S (GT86), and it's been doing that since I bought it new. It really sounds like a solid thump when you go from neutral to 1st at a light, and from 1st to 2nd at random times. When it first started, the answer everyone had was to change the transmission fluid. Since the car is easy to work on, and it was inexpensive to do so, I did put in Motul transmission fluid, and although it maybe got a little better (*cough* placebo *cough*), it's been doing it for the 30,000 miles I've owned it.
Toyota released a TSB on this, stating there wasn't a problem, and based on the limited number of issues I've seen with these vehicles (zero for me), I think it's accurate. Basically, the thump you hear is the clutch friction disc coming to a sudden stop when you shift into first gear. If you shift into neutral when coming to a stop but before fully stopping, the friction disc will continue to spin for a few seconds before coming to a complete stop. If you shift into first while the friction disc is still spinning you get the thump of the disc coming to a stop whereas if you wait until you come to a complete stop before shifting into neutral you will not get the thump. You will also get the thump if you're sitting in neutral at a stoplight with your foot off the clutch, then when the light turns green you quickly put your foot on the clutch and shift to first, you will get a thump for the same reasons as I said before.
Again, not sure if this is the exact issue you're all describing, but I just wanted to add the comment since I had been browsing the forums before making my final decision between a 75th Edition and a Trailhawk. Since I hate driving automatics, I'm going that route, and hopefully the issue is similar to what I experience in my Toyota since it appears to be a non-issue in terms of mechanical function.