Annoying When Saving Comments

Adobe Reader XI 11.0.2 on a Windows 7 machine
Exactly the same problem as the post http://forums.adobe.com/message/5044829#5044829, but there is no reply.
It is so nice to have all the commenting tools in Adobe Reader now. However, whenever I click File->Save for a file with new comments (not a protected file), it asks me to choose a path and a file name, which acts as a "Save as" command. Then I have to click the original file because I don't want to make an extra copy, so it asks me whether I am sure to replace the file. It is extremely annoying.
Am I the only one experiencing this problem? Can anyone help?

I appreciate your help. It works partially as what you described.
I disable all enhanced security (Sandbox Protections and Enhanced Security), then I can work freely with the "Save" for files in whitelist. However, for files outside the whitelist, after I add comments and click "Save", it pompts up a warning dialog saying "The document could not be saved. The file may be read-only, or another user may have it open. Please save the document with a different name or in a different folder." Then the rest of the story is exactly as what you said
I just did some more testing: it looks like you still have to do the Save As the first time you move or save a file to a new location. Subsequent saves function as expected, but the (for lack of a better term) Save-Flag seems to get un-toggled any time the file is moved.
I'm glad that it now works for files in whitelist. But my pdf files are stored in all different paths (EndNote did this). I can't add all these into the whitelist. Is it a way to apply the whitelist to include all its descendants?

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