Is your cl_restrict_server_commands 0? Try using rcon to run some mani commands directly.
It's impossible to set that command to 0 after the last update.
Ok, waffles. Let's work through this.
First off, are the following lines in your server.cfg?
exec mani_server.cfg
ma_war 0
Second, are the following lines in your autoexec.cfg?
mani_reverse_admin_flags 0
mani_reverse_immunity_flags 0
exec server.cfg
Third, is there a mani_server.cfg in your /cfg/ folder?
Fourth, do you have the all the necessary files in your /addons folder? These include the following:
mani_admin_plugin.dll - PC
mani_admin_plugin_i486.so - Linux
mani_admin_plugin.vdf
Make sure you have the .vdf. It no longer comes standard with mani and you have to use the .vdf creator accompanied with the mani files.
Fifth, are you using a version from the 1.2 series?
The 1.1 series is no longer functional after the update and the problem you are describing is EXACTLY the reason it is no longer funtional.
Sixth, what version of mani are you running?
I reccomend O or P, the last version released before he discontinued development isn't stable and he isn't' going to make it stable.
Once we have those questions answered we can get everything else looked at.