Okay, Jed, I have enough info to see what's wrong. First of all, the black/white splice is NOT a neutral connection, the two whites are. (I hope you haven't damaged the slave unit.) Lets's see if I can help you here:
Travelers always travel in pairs: three-way switches each have one dark terminal, the 'commons', and two lighter terminals, which connect to the travelers. One common is always hot, and the other common goes to the load; the travelers interconnect the two three-way switches.
When replacing three-ways, it's important to note which wire connects to each common terminal; marking them is even better. Too late, right? Okay, there's always hope. Here's what most likely was originally done:
The black/white splice in box #2 is the incoming hot (black) connecting to the white (still hot; one of the code exceptions) that runs to box #1, where it should have been connected to the common there, leaving the black and red as the travelers.
Ignoring the wires attached to the other switch, there are a black, red, and white from a single 'bundle' (cable) at box #1, right? These three wires were attached to the three-way, and nothing else, yes?
Back at box #2, the other end of the black and red travelers connected to that three-way, and the remaining black is the switched output to the load. So there should be two blacks and one red to connect there. Any of this sound familiar?
If I'm right, here's what you should do (with the circuit off, of course):
At the slave switch position (box #1), connect the white wire to the slave's neutral, the black to the slave's line (either one if there are two), and the red to the slave's yellow (traveler, remote, etc.)
At the master switch position (box #2), first undo all of your connections, and set the master aside. Disconnect the white (of the black/red/white bundle) from the black/white connection and connect it to the two whites already connected together; connect the black of the black/red/white bundle to the black you just removed the white from.
Now, pick up the master: add its black to the two blacks you just joined; add its white to the two whites you just joined; connect its yellow to the red (of the black/red/white bundle); connect its red to the remaining black wire.
This should take care of it. Let us know.
Larry
www.fineelectricco.com