Embedded PDF on web page fails to display

We have a number of PDFs that are shown embedded in IE (versions vary). This worked fine with Adobe Reader 9.5 but with 10, PDF fails to display.
Page takes a while to report error. Error:
There is a problem with Adobe Acrobat/Reader. If it is running, please exit and try again. (103:103)
I found a few other discussion similar to this in the forum but didn't find a definitive root cause.
In our situation, we found that if the user launching the web page runs Adobe Reader as standalone first, the error doesn't happen.
While workaround exists, I am trying to understand the root cause to see if we can correct this for all the users in automated manner instead of
mandating launching of Reader standalone as a prerequite step. Quite a few users using this web app.
Since launching of Reader standalone works, my guess is that some config/setup is done only after first use. I see that, for example,
reg keys are added under HKCU on first use. I don't know why first use from browser differs from first use from standalone though. Difference in
reg access? Enable/Disable browser plug-in produces different behavior so I don't think the setting is on the browser side. What other factors
may be in play here?
All ideas welcome. Thanks in advance.

Got a couple follow up questions. Postiing the response here.
1. Please send us step by step method on how to recreate the problem, and the URL of the PDF file that shows the issue.
* Write a simple console application that does nothing but starting a browser. Browser URL set to any web site with embedded PDF. I believe I used a sample on Adobe's site for last test.
2. Is everyone in your company experiencing the same issue?
* Yes, everyone can be affected.
3. Does the error show up on any PDF or just the embedded PDF?
* Only embedded.
4. Does the problem occur with Firefox?
* Not browser specific.
5. Do you have any other version of Reader or Acrobat installed on the same system?
* No, clean test box. Tested with 10.0.0 first. Failed. Then cleaned up install and installed 10.1.3. Cannot repro with 9.5.
Root cause appears to be Protected Mode. If I disable that, it works.

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