IE9 and Flash 11.5 and Protected Mode

I'm sorry that I didn't have the patience to wait for an answer in the other thread, but I am concerned that the other thread may be overlooked and I'll wait until the cows come home, and I am worried about security.
I received the Flash 11.5 update yesterday on my Vista Ultimate/IE9 equipped machine and immediately ran into problems with web pages not loading.
Firstly, that's not a pleasant experience when one is working against a deadline. 
Eventually, I find out it is because of you Adobe folks, and that isn't very nice to find out, either.  You folks seem to be a necessity on the Net and to mess up one of my machines and cause me to have to use up time to sort out the mess isn't very pleasant, either.  But you know that, don't you?
Okay, so I eventually find out I have to turn off protected mode in my IE9.
So how long is that going to have to continue?
What are the dangers when not being in the protected mode?  (Microsoft warns me with every page loaded, but I'm not turning that off, just yet.)
And I have another, distantly related question, if I may.  Many times I see the advice given around this tech forum to uninstall one version and install a previous one or reinstall the latest one and so on.  That is quite frequent advice.
Well, when the Adobe Flash uninstaller is used, does it clean everything out of the registry?
Thank you for your feedback, whomever you might be.

Try to uninstall Java with the JavaRa program and reinstall (32 bit) Java.
*http://singularlabs.com/software/javara/

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