You should state what equipment you are installing, so assuming you are working with the DS7000, here are a few things that may help.
As yancy stated, to start with, each base unit should be set to a different house code. But this is just for any lamps and siren that are to be triggered during a breach.
The remotes and sensors do not work on house codes; they have a randomly chosen security code. They have to be registered with a base unit. If one remote is arming/disarming 2 different base units, then it was either registered by both units or you have 2 different remotes that ended up with the same security code (1 in 64,000 chance).
You will have to reset and reprogram one of the base units. If you need to change the security code for one of the remotes, remove the batteries for at least 10 seconds.