I have the same problem.  I found a workaround -

Close IE

Open Adobe Reader as an application from the start menu

Under the Edit menu, select Preferences

Under the internet category, uncheck the first option "Display PDF in browser".

This will cause the pdf file to download and new window to open whenever you click on a PDF file (you may have to click the OK to download to allow the PDF file to download), but you should be able to save.

I found that some websites would not allow the file to download even though I clicked the OK to download button.  For those websites, I had to change the setting back to open in browser.  Also for those websites, the save button works.  Rather inconvenient if you go between the two websites.

 Source: http://social.technet.microsoft.com/Forums/en/w7itproappcompat/thread/643d0937-31ee-45f3-a73f-2c27c315d0a1