I have discovered what was causing one of the VFOs to tune slowly and I have also learned how to make my Flex controller work independently of the Smart SDR PC application. Both had been causing much head scratching!
The VFO problem turns out to be a known bug in the flex API, which results in numerous spurious messages about the status of the ATU being interspersed with response messages from the VFO tuning. These ATU messages should normally be very infrequent and they seem to take quite a long time to be issued, hence slowing everything down. For the time being I have unsubscribed from ATU messages and the problem has gone away. In due course I imagine that Flex will issue a new version of the radio's firmware that will properly fix the issue.
The matter of being able to operate the controller in stand-alone mode was mainly a case of understanding how Smart SDR works. I now know that SSDR closes all slices when it exits, resulting in, effectively, no radio. So the solution was simply to detect that there were no active slices and create one. There's a bit more to it than that and I am sure I shall find more things that I need to attend to but this is still a significant step forward in my project, as it means the controller can run in stand alone mode (possibly remotely) or in SSDR integrated mode.
In other news I spent a couple of hours this evening discussing the design of a PCB to go behind the panel for mounting all the panel controls with a pal who runs a small business doing this sort of thing. It would be a very neat solution but it certainly isn't a cheap option! It seems that it will probably have to be a double sided PCB and that adds cost to an already expensive prototype. I should have a quote in about 10 days and the ouch! factor will have to be evaluated at that time.