Well the Spektrum/JR 2.4GHz systems like most others are less susceptible to RF interference than a 35MHz system would be, but they are not anymore able to reject massive electrical interference than any other system. Usually..... If you get engine running glitches not present with the engine off with 2.4 systems, it tends to be spark related. That is things like a loose cap on the sparkplug, frayed shielding, wrong sparkplug like using a non-resistor type where a resistor type is required.

There are a few other documented cases of issues with 2.4 systems, but those tend to fall into the bad servo or extension category. I know you said nothing else has been changed, but I'd look for loose sparks first.