... This might have been part of your problem, or the design itself is somewhat unstable. What was the wind like?
I gotta jump in here. Several people have questioned if the design is "unstable".
I bought and built my Hyper Bat about two years ago, and if the design IS unstable, then my rocket is the exception to the rule. It flew well, and it performed just as it should have.
I also positioned both the booster fins and the upper stage fins in line, and experienced no problem. I would think if you "clocked" the bottom booster, say, 45 degrees, you might then be cramping the launch rod by a fin. Yes, I know, no two fins are ever in exact alignment.
During final assembly, I have to state that I spotted several errors in the instructions that I called to the attention of Estes. I spoke with their engineer long distance at their dime, for almost 20 minutes one day, and he impressed me with his frankness and attention to my concerns. Together, we reviewed the diagrams and he agreed that the diagrams of trying to glue in the upper motor mount had incorrect drawings. However, some common sense indicated that you could use the coupler and two taped motors together to get the correct "fit" or positioning. (I know I'm not being clear here, but I don't have those plans laid out in front of me.)
Also, there was at least one icon of glue that had come free in the instructions' paste-up before being sent to the printer, and that icon had "floated" over to another page, where it was obscuring a dimension or something minor. (**Remember this!)
In the course of our conversation, the engineer admitted that the entire instruction was going to be undergoing an over-haul because of the need to reprint the "TRI-lingual" short instructions. This would permit them (Estes) to sell in foreign markets. When that happened, they would be catching these errors.
I mention this so that you can check your set of instructions. If they are in 5 languages, you have the new version. However, if you have found the "floating glue icon"**, you can bet that your "following the instructions to the letter" has caused you grief.
All this being said, my personal guess is that your two stages were taped too tightly, as the cellophane wrap should melt through and allow separating very early on.
My first flight was on a B6-0/B4-4 and I'm pretty sure that I did a second flight with B6-0/C6-3 or something similar. I got five flights, two that were 2-staged.
As I recall, the booster stage did separate rather low... (30 feet up maybe?) and was on the ground very quickly, compared to the second stage, which floated down nicely with all further flights.
Hope this helped. And yes, you can find flight reports on
www.rocketreviews.com which indicate others have successful flights also!
Here's the direct link to my review, with the specific errors and corrections laid out for you:
https://www.rocketreviews.com/hyper-bat-3169.html