I'm extremely pedantic when it comes to this stuff, so sorry if my questions are a little pointed.
When you say "phone cord", my assumption is a flat "silver satin" style phone cable. The trick here is that, from left to right in the cable end, the colors will always be the same. There could be 4 or 6 conductors (or maybe
, but that's not really important. What is important is that the cable is effectively straight through.
If you have an RJ-49 cable running between the two rooms, it's very likely wired as an 8-conductor network cable. On these, the little wires inside the jack are wired in a way that makes the suitable for either telephone or network use. In other words, wires 1 and 2, 3 and 6, 4 and 5, and 7 and 8 are wired as pairs.
So - if you are using a "phone cord", you are using pairs 3/6 and 4/5. The RJ-11 jack will accept a 2, 3, or 4 pair cable.
If you used the same "breed" of phone cable, then the way you've described wiring it should be just fine.
The problem is that when someone has gone to the trouble of wiring an RJ-11 jack in their house, they seldom wire it to another RJ-49 jack - they nearly always go to a terminal block of some kind. Your installation could be different, of course, but this was one of the first things that struck me as you described the problem.
The other thing that you could be running into is that if this jack *IS* wired point-to-point, it is probably wired as a "two port hub" which means that pins 1 and 2 upstairs are wired to 3 and 6 downstairs, and 3 and 6 upstairs is wired to 1 and 2 downstairs. Pins 7 and 8 are probably straight through, as are 4 and 5. Note that this is how you would wire the connectors if you wanted to just hook two computers together through their network connections without buying a switch or a hub.
Without knowing more about how the two network ports are wired, it's not easy to identify the specific problem. If your ports are wired as a "cross-over", you can undo them using a short "cross-over" cable of your own and an 8 pin extension plug (8 pin, Radio Shack usually sells them).
For more information on the wiring issues you are running into, I've found a very nice webpage that shows what I'm trying to explain:
http://cableorganizer.com/articles/network-instructions.htm