I had the same issue for quite some time. Ironically, I upgraded from V1 ..... more prominent.
Update on my stalling issue.
The RD team went ahead and replaced my box to PT 3.0 and the bike feels much better. Apparently, the stalling issues seem to occur on bikes with electrical mods but 3.0 is calibrated/sorted to handle all that.
The 390 now feels extremely peppy with a constant slow speed RPM and no dips. The power output with the akra is maniacal! The stock dual-map seems to work well with my exhaust/intake setup, although, I'll be going back to them for a custom tune & traction control.
I've installed a map switch next to the console and this makes it extremely easy to switch between the 2 maps.
A great thanks to the RD team, especially Karthik, for taking the time in helping sort these issues.
P.S. Can't wait for the RD quick-shifter to become available (3.0 is QS compatible!)