Are they identical controllers? (I would assume so, given the thread this is in, and that they are this thread's titular type, but....)
There are some controllers like my EVAssemble unit that appear to only work in the "demand speed" mode, which is where the throttle also controls braking even if brake is not engaged, if throttling down below the speed the wheel is actually at.
I am not sure if the Xie Chang (Infineon) controllers have this mode or not--I have not used it on mine, just regular regen braking. The two working ones I have are a 6FET from Lyen and a 12FET that I think was an Ecrazyman. Both are nearly identical, except the 12FET does not have the X3 pad, IIRC, and so there was something in it I couldn't do and test (which I can't remember what that was right now; I'd have to look it up in the CrazyBike2 thread).
If both of yours are identical newer Xie Changs, then with identical programming they should behave the same. If they don't, then my first suspicion is that they have different firmware revisions, and/or there are EEPROM locations in the MCU that are not writing the values you are sending, for whatever reason, in one of them.
I can't think of a reason for a difference in behavior besides that, as any kind of hardware problem outside the MCU would probably cause some other (most likely obvious) problem.
I suppose that if the battery pack voltage on a controller was high enough, that regen might engage but not actually produce any drag, as no (or too little) current would flow back to the battery.
Similarly, if the motor's BEMF voltage is too high, the controller will probably prevent regen to avoid damage to the controller itself.