Minecarts with (named) ghasts travelling in a constant loop will sometimes lose their velocity, appears to happen on chunk borders so I suspect it is because the chunk they are entering has unloaded. Does not always occur, cannot be reliably reproduced, but has happened repeatedly.
Is this still an issue in the current Minecraft Snapshot 15w45a or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.