I was wondering if this has happened to anyone else.
When you select Manual for all options, the game still auto subs, auto scouts, calls up/sends down players, auto corrects batting order, etc.
This has been an issue since release, however I'm trying to see how prevalent it is, so that I can make a report to SDS with hopes of a fix. It's completely ruining Franchise mode by taking the fun out of having full control over an organization.