For me, it is a 100% failure rate of the auto updater. Until they release a new version and the auto updater actually works one time for me, I am going to have to go with saying it does not work. Not sure what you meant by "and its been left because v4.0.1 is delivered most of the time." 4.0.1 was not delivered to anyone, everyone had to manually seek it out after being told it exists (the download site does not reference 4.0.1 anywhere).
If it really is just a simple error in the way it was entered, they could have removed it from the delivery system and entered it again properly. But no, it still is not auto detected, quite a long time after it came into existence. That tells me their either do not care enough to fix something they know is wrong or that the auto updater actually does not work properly. Neither one casts S3D in a very good light.
My guess is the updater only works on the first two digits, X.X. So it sees 4.0.1 the same as 4.0 since it does not look at the third digit. The only ways to fix this is to program the updater properly to look at all the provided digits or only use two digits in the file number. This would explain both why it worked in past (I can only trust your word on that, having never experienced a working updater) and did not work now, and also explains why they did not fix the loading of the update - they simply cannot with that version number.
That is the only thing I can think of that does not make them look uncaring or inept. Of course, it still means they did not care enough to update the download area with the new version number...