According to Bethesda the second patch should fix autosave and quicksave issues, apparently this problem was not noticed prior to release because it was such a difficult thing to replicate during beta testing.
To fix these problems Bethesda has been forced to turn off the Steam Cloud functionality, from what we can see it will not be turned back on until developers are confident that it won’t cause any more problems.
If you have not yet received the second patch you need to restart your Steam client, if you would like to find out more about the second PC patch check out the source link below.
Have you installed this second patch? If so, has it fixed all autosave and quicksave issues?
Also See: Fallout 4 news not coming for Christmas