Not a bug: Native and Docker MySQL volumes are separate. ~/MacFullStack/www is shared; databases are not. Docker is not “more correct”: it is a second runtime for special cases, not an upgrade from Native.
Before a lasting move: macstack db migrate-runtime --to docker (or the Settings dialog). Redis is not copied. Dumps in ~/MacFullStack/dumps are left alone — restore from them by hand if you need to.
For day-to-day work, switch back to Native — that is the product, and Free is built that way. Turn Docker on when you need isolation, not “just in case”.
Help: /help/migrate-runtime.