Sometimes carriage returns get through after I write a trigger to gag a line of output from the mud, but I'm not sure why. Most of the time, they don't.
Could it be something I'm doing differently in the trigger pattern?
It is quite a vague question, and I don't have a definite answer. Nick probably does, but I'll give it a shot anyhow.
First of all, you have no other conflicting triggers that do get it logged?
Second, is the newline per chance arriving in another packet, or is an extra newline somehow arriving? Perhaps MUSHclient somehow gets confused, I don't know.
It would probably be helpful if you could give the trigger in question, and some output with the Debug Packets function in the Edit menu of when it does happen, and does not happen. This would give us more information as to what could be causing your problem.
I have seen this a bit when playing with Aardwolf triggers. Basically the reason it appears to let extra lines through is that the lines are actually there - because the MUD sends a newline when it thinks you just had a prompt. One workaround is to make a trigger that omits multiple blank lines - I think there have been a couple of posts recently about that.