There are a possible two problems you might have. First a quick explanation of 3-way systems. If you have a common 3-way system, one switch box will have the "Power End" and the other switch box will have a "Switch Leg" end (the wire that goes to the actual light fixture. Then inbetween the two boxes there will be two (usually red / black ) "travelers" that connect to the switch. http://www.electrical-res.com/EX/10-19-02/3-way-switch-wiring-diagram.jpg
Here is a link to a standard 3-way system. In the picture, the switch on the left is the "power end" and the switch on the right is the "switch leg" end. the first thing to do is establish whether you are in the "power" or "switchleg" box. You can do this by completely disconnecting the dimmer, then test which wire has power using a voltage meter. (do not use a "hot stick"! the tester that beeps or lights up when it senses voltage. These can give you a false reading) Once you know which wire has power, go to the other switch and flip it. If the same wire still has power, then you are in the "Power" side of the 3-way, IF A DIFFERENT WIRE HAS POWER NOW, YOU ARE AT THE "SWITCH LEG" side of the 3-way. The most frequent mistake made while installing a 3-way switch is getting the common and travelers mixed up. If you are in the "Power end", the "common" (or connection to your dimmers black wire) should be the wire that had power no matter which position the other switch is in. If you are in the "switchleg" box, the "common" or black wire from the dimmer should connect to the third wire that DID NOT HAVE POWER no matter which position the other switch was in.
The second (and less common) mistake with 3-way systems and dimmers is that certain dimmers are REQUIRED to be on either the power or switchleg side to work properly. If this is required it should be stated in the instructions!. Good luck and feel free to reply if you're still having trouble getting it going.