I too have seen this problem.
I don't think the problem is with the FTDI Driver as they are generally rock solid and are in use in thousands of products around the world. It is probably THE most popular usb-serial chipset in the world. Having said all of that - it could be that their latest driver, or one particular version of it, behaves slightly differently than before.
As the contributor above states, there is an exception thrown by PicoScope while enumerating the USB devices and this seems to be an area worth investigating. It would be good if PicoScope could catch this exception and handle it, rather than terminating. Especially considering that it is enumerating non-pico devices at the time, so it should be able to happily ignore the mis-behaviour.
I'd love to know when this issue is addressed, since by nature of my products I have to have both pico and several USB-SERIAL convertors in use at the same time, and it's a pain having to unplug all the serial devices before starting PicsoScope.