That "Sloshing" can easily be prevented by using Shutters. So that's no problem
Let me be more clear then... GT Fluid pipes do not work right, even if you use shutters everywhere. LOL If others can get them to work, then they're smarter than I am (no surprise there). I use Ender IO conduits because they work right every single time (despite your reported glitch).
As Pyure said, I think the only time when GT Fluid Pipes would be acceptable is in slow processing lines where the conduits will always be "full" or "stuffed" or "pressurized". The instant there is any space whatsoever in a GT pipe, that's when the problems begin, and I don't care how many thousands of shutters you have installed. LOL
I've been told the game is performing a calculation for each individual GT pipe segment, in essence the program views each pipe as an individual tank, and thus it has to perform calculations for each segment, for fluid to go back (and perhaps forth) between each segment, and that's why my assumption is that GT fluid pipes require many more calculations that Ender IO conduits do. But I guess I'm told that's incorrect, so... good luck if you use em. hehe