I've just tried the #hist~int~10 (and other values) setting and not getting this problem. Does this problem happen if you send the message directly from the on-screen message sending entry field?
I will send you a link to the latest .exe in case it was a bug that was fixed but has yet to be released. Please let me know.
The port control messages are no more than ordinary messages to the Arduino and only have the meaning that you can see in the message handler vDoMsg(). I'm not expecting an issue here but, hey ho, stuff happens. I would expect the Arduino to not send data if the port wasn't connected irrespective of whether there is an unconnected ESM somewhere in the mix.
Try renaming these messages in vDoMsg() so they don't get invoked and let me know if it clears the problem. Also how much data is collecting in the port? Have a look at the number on the title bar of the ESM form and see if its getting big (bigger). That might be the issue.
Perhaps a 32u4 needs to be told not to send data..., I don't know, I'm not familiar with it. However I wold have though it would be a problem with the Arduino IDE's own monitor. May be someone knows something about these.