I am using the IRC client Irssi on Debian.
My bot is written in PERL and I have it send out the raw command when it parses !timeout or !purge .
No messages get purged and they do not get timed out for x seconds.
So that has to be an issue with Irssi, have to look into that, more debugging yay!
EDIT: fixed by appending ‘:’ before the user’s nick in the send_raw function.