(Following on from https://acquia.com/network/node/36861.)
Using Acquia Marina as the base theme, though these issues are probably not related to the theme.
Encountered the following glitches:
1. For some reason, the base theme's regions are not inherited. This is a bit odd, given that a) most other things inherit nicely, and b) inheriting regions would surely be the expected "default" behaviour. The workaround is to copy all the region definitions from the base theme's .info file. If you don't do this when first setting up the sub-theme's .info file then all active blocks will get assigned to region "left" and you end up having to set all your blocks up again.
2. The sub-theme has a setting for "Secondary links" on the theme's configure page, whereas the base theme doesn't. Not sure yet what the significance of this is.
3. If a custom title is given for a block then it is not displayed unless you hit the configure link for the block and re-save it.