Trouble with Protected Mode whitelisting and file links

Question

Our system details first: Adobe Reader 11.0.7, Windows 7 SP1 32bit, IE9
We have some documents that contain URLs (file://...) which point to other documents (mostly PDF and DOCX files) on the local harddrive or on remote network shares. Those links work perfectly fine when Protected Mode is turned off - you click on it, IE opens and displays the document (PDF) or prompts you to open/download it (DOCX). As soon as you turn on Protected Mode those links stop working completely and I can see an access denied entry in the AdbeReaderBroker.log. All as expected.
Where it get's weird is that the links still don't work even if I whitelist nearly everything. I can click on them and nothing happens, they don't even generate an entry in the broker logfile anymore. Just so you have an idea, here is my current whitelist used for testing:
FILES_ALLOW_ANY = \??\C:\*
PROCESS_ALL_EXEC = \??\C:\*
REG_ALLOW_ANY = HKEY_LOCAL_MACHINE\Software\Adobe*
REG_ALLOW_ANY = HKEY_LOCAL_MACHINE\SOFTWARE\Adobe*
REG_ALLOW_ANY = HKEY_CURRENT_USER\*
And here's everything contained in the broker logfile (including when I click on links):
[07:07/15:29:57] Adobe Reader Protected Mode Logging Initiated
[07:07/15:29:57] Found custom policy file: C:\Program Files\Adobe\Reader 11.0\Reader\ProtectedModeWhitelistConfig.txt
[07:07/15:29:57] Adding custom policy: FILES_ALLOW_ANY = \??\C:\*
[07:07/15:29:57] Adding custom policy: PROCESS_ALL_EXEC = \??\C:\*
[07:07/15:29:57] Adding custom policy: REG_ALLOW_ANY = HKEY_LOCAL_MACHINE\Software\Adobe*
[07:07/15:29:57] Adding custom policy: REG_ALLOW_ANY = HKEY_LOCAL_MACHINE\SOFTWARE\Adobe*
[07:07/15:29:57] Adding custom policy: REG_ALLOW_ANY = HKEY_CURRENT_USER\*
So the policies get applied, Protected Mode isn't blocking anything anymore, the links still don't work and now I'm out of ideas. I also tried all of this with the Trust Manager setting "Allow opening of non-PDF file attachments with external applications" turned on, same situation.
I hope someone here can point me in the right direction, maybe I'm missing something completely obvious here.
Edit for people having the same issue:
After some further testing it became clear that the issue only occurs when the PDF containing the hyperlinks is created using the built in PDF generator of Word 2010. PDFs generated with Adobe Acrobat Professional work just fine and can also open the applications directly without opening IE first. I'm not sure about the exact difference in the generated link, Word seems to generate file:// URLs which I can access with right click -> Copy Link Location, something that's not possible for the links generated by Acrobat.

Answer 1

Maybe the information http://samwel.tk/laptop_mode/faq might help.  Particularly #3 and onward.
I only use powerdown. Thread = https://bbs.archlinux.org/viewtopic.php?id=134109
packer -S powerdown
substitute packer with yaourt or do manually if you wish so.