Hmm, I'm kind of in the process of doing the drop-target retrofit myself. Kind-of because I am making very slow progress.
I will also be using the leaf switch style drops, but my understanding is that, to work properly, the 'all down' switch connections must also be wired. (See http://pinball.flippers.info/firepowerdroptargets/.) I would guess that you have not connected them because there is no easy way to do so with non-horseshoe drops. I suspect that the behavior you are seeing is caused by the MPU missing one or more drop target hits (which are meant to be momentary). At a guess, I would say that this is caused by row/column collisions with other switches.
I would be interested in knowing exactly what behavior you are seeing if you have the time and patience to test it out.
One of the reasons for my slow progress is that I am working on some circuitry to simulate the momentary and 'all down' behavior of the horseshoe drops. I wish I could say that I have an expected end-date for my project but I don't. I suspect that the fastest solution to your problem will be to downgrade to horseshoe drop targets.