I use the FlexiPrint RIP on an HP Latex 330. To be honest, I really don't care for the program at all, and I frequently have issues with it (like the way it auto-tiles nested jobs, and so if you are printing several wall-covering drops that need to be in order, they will be all out of whack and won't be consecutively flipped like you need them to be, but I digress....).
Have you tested this issue on different media types? I have seen nearly this exact issue on DreamScape Matte Vinyl. I tried cleaning printheads, checking the optimizer ink levels, running a substrate advance plot, making sure the printheads were aligned, basically everything you can on the printer.
Needless to say, the issue was merely with the coating of the media. For me, the issue did not occur on any other kind of media, and it has happened on multiple roles of DreamScape Matte Vinyl.
To me, that doesn't seem like the RIP would do anything differently to affect the coalescence of the ink. You can try using a heavier ink density on your profile, but I doubt that will really help. You could also try to increase the amount of time between each pass, and increase the number of passes. This may or may not make a difference.
I'm actually really interested in this because I have seen this exact same issue and to be honest I have no idea what it is, either, and I even sent a sample of this issue to HP for them to look at and figure out. But replacing the media solved it for me. :/