Lightroom 4 - Catalog problem?

I recently installed Lightroom 4.0 on my new Windows 7 Home Premiun SP1 (64 bit) computer and imported my Lightroom 3.6 catalog into a Lightroom 4 catalog.
I have two problems which may or may not be related.
First:
While working in the Library, adding key words, etc., Lightroom will suddenly report in the current photo "The file named "xxxx (either .mrw or .jpg)" is offline or missing". On viewing the folder listing in the left-hand pane, all of the folders display with a "?". They did not do so moments before.
Second:
My LR4 import path is C:\Users\Bain\Pictures\My LightRoom.
However, Lightroom is displaying the folders imported since the upgrade as if they are in the root of C:
When I view the folders in Windows Explorer they are displayed properly in the My Lightroom folder.
I'd apprecaite any suggestions or help in resolving these issues.
Bain

Thanks for your reply Brett
Let me clarify the issue of the Missing Folder.
1.       The Lightroom 4 folder listing is normal
2.       While working on a photo in a folder I receive the "The file named "xxxx (either .mrw or .jpg)" is offline or missing" message.
3.       All of the folders in the folder listing are displayed with the question mark “?”.
4.       This issue has occurred multiple times.
I worked in Lightroom until I was able to recreate the “offline or missing” message, and all the folders in My Lightroom displayed ‘?’
I followed your instructions, right-clicking on the folder the error occurred in, selecting Find Missing Folder and browsing the  folder location, the folder view flickered, but all folders continued to display ‘?’.
While I was typing this, the folder listing in LR ‘refreshed’ and the folders no longer displayed ‘?’
As you can imagine this is extremely frustrating.
Bain

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