I'm not sure it's some configuration I have on synaptic (maybe having the stable-security as the prioritary release? I'm not sure it's set as such, though), or some inherent difference between both (I used to think it was just a GUI frontend to apt-get that would do pretty much exactly the same, once you click to "apply" at least, but it may not be the case), but in some cases synaptic will fail to install some packages, and not really give an explanation why. But the very same package...