i have a mikrotik BS that i use to connect clients using 2.3 frequency range. there is a certain site which is less than a kilometer away from the BS which keeps on disconnecting. i have tried changing the antenna at the client side as well as frequencies but that does not help. The antennas work perfectly when i move them to a different location.

How strong is the signal ? and what about ccq?
signal -77 dBm
CCQ -77 dBm
what protocols are you using?
Upgrade to the latest Router OS (Ver 5.4 as of this typing) and test again.