FrostG -- if you are scanning in 3F, the software can semi-intelligently make separate scans. It does not do this through any optical detection, it does it by scanning a certain length of the holder and designating it a single image. So when you use the six frame holder you need to make sure that the first image is lined up to the top edge of the holder. It will scan so that the images are a bit longer than a normal 35mm frame, so that it gets all the image. Then the auto-frame detection will crop the excess so that the selection just goes around the image. This works well with cameras in good shape that have regular image spacing and well-exposed frames. It does not work well if spacing is uneven, or if frames are too dark (the auto-cropping will crop out the dark edge, if for example the bottom or top of your frame is very dark from some reason...a dark foreground or a dark sky in a night photo etc).
Since the system is not based on optical detection, it also does not work for non-standard sizes, unless you go and create your own frame sizing standards (which you can do in FlexColor). So your 6x6x3 holder will not automatically scan 6x7 or 645 frames unless you make a new holder measurement for it, and tell FlexColor to use that one. The good news is that if you are using standard 6x6 or 35mm with good spacing, these holders will save you a lot of time. I do it a lot. I can scan six frames at a time for 35mm, with just one press of a button (on the X5). Since it is 3F, you can just go back to it when it is done, and slightly tweak things and resave the final Tiff if you need to change something.
As for service, I agree that once a year is overkill, particularly in a non-production environment. Service is expensive. I would say don't bother unless there is a problem, or maybe every 3-5 years. If the service dialog is bothering you, I think you can turn it off in the debugging feature of the scanner.
If you open flexcolor with the scanner on, type "debg" all in a row, it will give you access to the service tech's menu options. In the maintenance section, I think there is an option to turn off the warning. Another very useful feature is the monitor window...that will give you a live readout of the light hitting the CCD. If there are any large valleys in the readout, it is indicative of a piece of dust or something in the way of the light path. This will manifest itself as a dark bar running through your scan. Try blowing air in there until it goes away. Hopefully it will take care of it and save you a trip to service! You can also do a CCD calibration in that debugging menu. Don't mess with it unless you have to, but it can also be a life-saving tool if you need it, again, saving you a few hundred bucks in service/shipping etc.
While they are not perfect, I have found these scanners to be the best option on the market. For me, their combination of speed, performance, lack of need for glass or oil mounting and compatibility with currently available computers and operating systems makes them a much more attractive option than anything else out there.