Acrobat Pro 8, Highlight not working in browser

The company I work for has a specific audience that requires functionality in Acrobat Pro. This audience accesses these PDF document on our intranet using IE6 and uses some of Pro functionality (highlight, stick notes) and saves the annotation files locally. All that worked well with Acrobat Pro 6.0, but we recently upgraded to Acrobat Pro 8 and all these users are seeing is basic functionality, similar to what is in Reader. NO more annotation features.
I have verified and Reader is not installed on these workstation, a clean install of Acrobat Pro 8 is installed. If I open a PDF outside of IE6, Pro opens and all the functionality is there, but in IE6 it is limited (Reader Like). I have attempted to add the tools to tool bar but after selecting tools, they do not appear. Browser just refreshes without tools, as if they are being prevented from loading.
Has Adobe changed the functionality of Adobe Pro to only allow in browser viewing of documents with something like Adobe reader? I have searched the web and have seen nothing about this. Please help.

I am not sure if VISTA has the same problem as Win7 or not. For Win7, the AcroTray application that is used for PDF creation (both when printing to the Adobe PDF printer and with PDF Maker in AA6) will likely not work correctly. This may also be the case with VISTA. To get around this problem you have to print-to-file (you can change the PDF Port to FILE in the printer properties). After the file is create, you can open it in Distiller to complete the PDF creation. It may be possible to create watched folders to automate this process, but is not as ideal. In any case, you will likely have to use a work around. Also, update your AA6 (currently at 6.0.6). I have been able to do this with AA5 on Win7 as a test and it did indeed work. There may still be other issues for AA5 on Win7, but that was the major one.
All of these changes came from the rewrite that Adobe had to do to be compatible with the new OSs, not a trivial task. Do you want to blame Adobe or MS or both? Take your pick, but the end result is that it is time to upgrade. Unfortunately, AA6 can not be upgraded to AAX. You have to buy AAX at full cost at this point. To get the upgrade you would have to have at least AA7.

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