I've never had that text box problem, might just be you--I know I get UI ghosts sometimes if I migrate settings from one machine to another, if you've been porting settings for a long time there may be something incompatible with later versions that needs to be removed. As to the second, and you probably already know this as a longtime user, you have to click on Flash to "activate" it, such as needing to hit the play button twice on a YouTube clip, but then once Flash is in focus you can adjust volume, pause, etc. without needing a second click. Maybe this is your issue--being active in Flash and not in the rest of the page would do something vaguely similar to what you describe.
I hope Opera doesn't start to suck, I've been using it for over 10 years and none of the other browsers have the options, configurability, or ease of migration to new installs/machines. Chrome is okay, I guess, but I desperately hate the UI. The main reason I stay with it, other than its general greatness, is how responsive the UI is to input, even if it's doing things at the same speed as other browsers it just has a tactile "fast" feeling.