Currently Pipes'n Physics also works really well with FlowingFluids, it just needs some tweaks.
One major thing I came across is when having two ponds, one empty one full, if connected by a pipe, 1/8 of a source block will flow over to the empty pond (in my case I just had 1x1x1 empty and 1x1x1 water connected with a pipe), after this 1/8 of a source block reached the other side it stops leveling out.
I assume it simply is because the code doesn't take less than a full block into account and just checks "water 'block' is already directly after the pipe => no more further leveling required"