PoE Lower Signal Voltage
I don't know how it works but it works even if it is clearly not safe.

Here is a capture from the Raspberry Pi Schematic v2.1 as on the official website. You can see the Ethernet RJ45 jack with the integrated magnetics and terminations:



I'm assuming you haven't connected anything on the left side as this is the components side and 48V will break everything.

Mode B should work more or less because there is no transformer on the pairs, but you are lacking serial capacitors before termination resistors. These capacitors are used to block DC part between each pairs.

But you use only mode A and putting the DC voltage directly on the wires of each pair is not the same as putting it on the center tap of the transformer (red circles). And as you don't have access to the center tap of the integrated magnetics, you won't be able to use Power over Ethernet with the RJ45 port of the Raspberry Pi.

At the beginning of this Application Note from TI, you have some information about Power over Ethernet and Ethernet magnetics which are PoE capable.
Also on this schematic you have an example of Power over Ethernet with the same type of magnetics design as the Raspberry Pi one (but in a discrete kind and not integrated in a RJ45 port) : http://media.digikey.com/photos/rdl/tps23754evm_420_schematic.jpg