I work in the computer world, and when you are create an new version of a software, you must create a program to update old versions... I think there is a bug in the Update in the SD1 from the 3.0 to 4.0a, and the 4.0b don't fix this bug (if you only install the upgrade). You must reinstall the 4.0b entierely with all disks...
This is just a supposition... I m not sure ...