I am having the same issue. I´ve tried to render the effect as well as to try various Strobe Operators but nothing seems to work. Do you have any additional troubleshooting steps that I should try or a different effect that works like this one? Thank you.
I just ran into this problem but I didn't really do anything other than here are my settings that I ended up using. Settings: 50% blend, duration 0.20, period 0.40, random strobe probability 75%, makes layer transparent, Operator Screen, seed 0. It seems like it was the probability number that was giving me trouble. Once I moved that up the effect starts showing. I also did NOT have to render after every change.
Encoutnered the same problem. Solution to my problem was that the clip was at 50% speed. To fix I just exported the individual clip brought it back into premiere as a standard Mp4 clip and then re-added the strobe effect.