I misunderstood your previous post, I thought you were referring to the VCP advanced options, not FM.
I WAS using version 7 something, but upgraded to 8.18 after reading your last post. I tried the advanced option to disable them completely, and here is what I'm getting:
On the very first open after plugging in the board, the lines are asserted and my board resets. I can do this by trying to read the device signature (which will fail, but is expected since I have it disabled). Every operation after that will NOT assert the control lines, so obviously FM is simply leaving those signals disabled when it closes the COM port. But that very first operation after a plug-in is still asserting the lines.
I don't know if this problem is solvable (with software). It may just be built in to Windows to assert those signals whenever the COM port is opened with default values. But I guess you guys should at least know that the option to disable those lines completely won't work on the first operation after a plug-in (at least for an FTDI device).