in your plugin configuration file add
timeout 120
or on a per plugin basis in plugin-conf.d
[plugin_name]
timeout 120
There is more black magic going on, it seems the munin-update polls every 10 seconds and timeout after 2 minutes so any timeout > 2minutes on the plugin side has no effect. I'll check for munin-update timeout.
Seems like a long time but I do have issues where plugins take a very long time and can't find the root cause, the problem is on centOS when a plugin timeout it becomes orphan and takes 100% cpu :(
If you had this problem and found a solution I'm a taker...
--Gilles