If you find that your outgoing lines are shown double, you need to fix your :input: statements.
For :input: you need to perform 2 steps. First, as above, search for :input: in your other scripts (not the mircryption script!) and insert the following after the last ':'
if ($halted) return else
so, for example:
on ^*:text:* single_command_here
becomes
on ^*:text:* if ($halted) return | single_command_here on *:input:#: {
becomes
on *:input:#: { if ($halted) return
Second, you need to make sure the MircryptionSuite scripts are executed before any other existing script. You can do this from mirc, by hitting alt-r, then selecting the Remote tab, than File->Order. Then find the mircryption related scripts and move them to the top.