I'm sorry but it's still unclear, when I try to send a long line from the editbox (but let's assume it's the same as /msg from your script), it produces two (let's assume the split gives two parts) PRIVMSG in the debug window, this is correct and I can only assume that a /debug -i alias would properly catch those two PRIVMSG and try to /msg them somwhere else.
I could assume the origin server has the same line limit as the destination server and you have more or less the same length for your host in both servers etc, meaning it shouldn't split any of these relayed messages.
Now you're saying that it does 'resplit' them? So my assumptions above would be wrong but as far as your script is concerned, it relayed correctly, no?
But now comes my confusion, you say:
The first part is ignored by code in the debug intercept
To me this means the first PRIVMSG in the debug alias is not caught properly? That would be a bug, either in your script or with mIRC..?
but the second split part is seen as a new message and is relayed again
This is just non sense to me, it is suggesting you're first catching the whole messages with the first PRIVMSG, which is impossible if a split happens, and then that there is still a second PRIVMSG with the correct 'second part' of the split, which would explain why you say it sends that second part again, but this is all impossible unless your script is buggy or mIRC is.
Your screenshot is useless to say the least, can you provide a real example and/or the debug of what is actually passed to your alias (it looks like there might be a bug here, i didn't try this), the best would be to pastebin your script entirely so we can test it, with the exact first whole line you're sending.