Actually, in the first picture, it looks like you're not directing the fluid, which is why you're getting backup. BC is fine as is, it just requires some thought, which TE does not. TPL has said he has no problem with adding some thought into more complex systems, such as what you're using. Try putting an iron fluid pipe in to direct the fluid flow, because it looks like it's trying to input water into the other emerald pipe since BC randomly chooses directions at cross-sections if there's nothing set for directions, like an iron or diamond pipe.If you want a quick summary, buildcraft pipes have always had really odd behavior when you try to have multiple outputs or loops. Here is an example in pictures:
This doesn't work: http://puu.sh/hoizU/c2b9285d3b.jpg
But this does: http://puu.sh/hoiX3/a373b01c65.jpg
It is the exact same output to the system (80mb/t) and the exact same usage (4 combustion engines). However the first setup will let 3 engines go dry and the second works perfectly. It's just how BC handles stuff and it's dumb. I assume BC 7 will be a lot better but we're stuck with 6 for now.
I'd hardly say that I was ranting, and just because the pack ships with or without mods doesn't mean anyone who is annoyed can't just change the list themselves.