Dear Gunderic,
Let me try to help you answer to both your query.
1. When you are installing Flash player, it prompts with option in the end stating "Auto update" or notify before installing updates. So you can check for notify before applying updates.
Alternately, you could set the Flash player update flag to False. Please take proper backup before.
Hkey_Local machine->Software-Macromedia.
2. This could be likely due to change in the Flash Player security. Most likely the upgrade of Flash player could be reason for this. There are at times Adobe will introduce additional security which might require you to update your global security setting.
Let me know if this helps.
Regards,
Amit