This problem is due to Cisco bug ID CSCse75035, which also mentions that IP fragmentation prevents the access points (APs) that attempt to join in Local and Remote-Edge AP (REAP) mode.
Though this bug refers to access point it could be considered since bug is on WLC.Current version of Controller cant reassemble more than 2 fragmented ip packets.So if network between WCS and WLC has a small MTU such that the incoming IP packets had to be fragemented more than 2, WLC might not join WCS.This problem occurs if WLC runs version 3.X or Less.This is fixed in the version 4.0 because it can re-assemble upto 4 packets.
Also, it is important to make sure that the controller code and WCS software versions are at the same levels. For example:
WLC version 22.214.171.124 = WCS version 126.96.36.199
WLC version 188.8.131.52 = WCS version 184.108.40.206
An AP that runs old code, for example 3.2, cannot join a controller that runs 4.0 code if the Maximum Transmission Unit (MTU) is less than 1500. This is because specific code exists in order to handle a REAP connected to a controller with an MTU value of less than 1500. In the REAP case, it is always assumed that the MTU is less than 1000. This avoids re-fragmentation from the network as both the AP and the controller cannot handle more than two IP fragments. When the controller is upgraded to version 4.0.x.x, it sends the Join response with a larger MTU because it assumes that if the network re-fragments, the AP re-assembles. The AP still runs old code, so the issue occurs.
In order to fix this problem, take the AP version into account for the REAP case, and use a lower MTU until the AP joins the WLC. Then, upgrade the code.
Note: IP fragmentation prevents access points (AP) that attempt to join in Local and REAP mode 4.0. This problem is fixed in version 220.127.116.11.