We are having the same problem.  We had this problem a few years ago when upgrading Notes 7.0.2 clients that had Acrobat 8 and 9.  We upgraded them to 8.5.x and it broke.  We found that once you go to 9.1, that it works again.  Now, we have many 8.5.x users that have Acrobat 9.1+ to use the PDFMaker utility.  Once we upgraded them to Notes 9.0, it broke again.  We have also tried the latest version of Adobe Acrobat 11.0.3 and it still does not work.  We've added the same three lines in the notes.ini, verified the dll file is still there and the client removes them upon startup.  As a result, we have had to stop upgrading these clients to Notes 9.0 and revert some back until there is a solution. 

Is there a manual workaround to get this to work that anyone knows of?

IBM made some changes to the code in Notes 8.5.3 Fix Pack 5 and higher that seems to be blocking the Adobe toolbar.  That toolbar has caused a lot of issues for IBM and Adobe has yet to fix it.  So IBM implemented their own fix for the issue.  That fix seems to be that they now prevent the toolbar from loading at all.

Now, the rest of the integration still seems to work, at least with 8.5.3 FP5.  So the options that are on that tool bar are also available in the Actions menu.  Apparently, the issues between IBM and Adobe all boiled down to that tiny two button toolbar.

I have not yet tested Pro X or Pro XI with 9.0.1 yet.  So I do not know if IBM went even further with their own fix in 9.0.1 or not.