First, try connecting only the CDJ-900s by PRO DJ LINK. If there is a conflict between two players, both their numbers flash, so you can tell there is a problem between those two players.
Next, to avoid the type of confusion described below, when connecting CDJ-900s to the DJM-2000 by LAN, connect the CDJs to the DJM-2000's "channel port".
The DJM-2000 has two types of LAN ports, a "channel port" (for CDJ player connection) and a "PC port" (for computer connection), but the "PC port" can also be used to connect CDJ players.
For example, if a CDJ player is connected first to the "PC port" and it is say number 2, then another CDJ player is connected to "channel port" number 2, only number 2 for the CDJ player connected to the "channel port" flashes, making it difficult to know where the conflict is.