I am not sure why this is happening to you, it really shouldn't. The Web page with detailed instructions on how to set up a DD-WRT Repeater is here. The key point is that you are told to use for the client Repeater's wifi network, a name that differs from that of the main router's wifi network, to which you are trying to connect your Repeater.
In other words: in the Wireless -> Basic Settings tab, Physical Interface Section,
you must fill in the name of the wifi network you want the Repeater to connect to, including connection details (password, channel); let's call this network Wifi0. Then, in the same tab, but under Virtual Interfaces Section you are supposed to provide the details of the new wifi network, (let's call it Wifi1), about which you are told:
Wireless Network Name(SSID) : Different from Primary Router
Now suppose you add another repeater. You will tell it to connect to Wifi0, and you will setup a new network Wifi2. If you have followed these instructions, then they should not connect to each other at all.
Two small comments: make sure you pick distant channels for all of your wifi networks, depending also on your neighbors' interference. For instance, if neighbors occupy channels 6 and 11, use 1,4,9.
Secondly, it might occur that your repeaters just remember the networks they managed to connect to in the past. In this case, do a Factory Reset (Administration -> Factory Defaults) and repeat the set up.