I am unable to recreate either of these issues; in both cases RM9 works as expected.
Assuming that you’ve run all of the db tools already, for #1, RM settings are stored in a file called “RootsMagicUser.xml” and it’s located in a separate folder from user defined folder structures. On mac, the path to the xml file is ‘{HD name}/Rootsmagic/Version9’. Windows should be something similar. If you aren’t comfortable with viewing/editing xml then it might be simplest to reset your system settings from the command palette or try a de-install/re-install of RM9. (Note that resetting system settings sets them all to default values so you might want to do a few print screens first.)
Issue #2 seems more complicated. You may want to describe your linking steps in more detail or go right to opening a ticket with RM support.