SCCM 2012: Problems deploying x86 software on x64 systems
For acrobat, I believe they changed the way setup is run. We are using the exe instead of the msi. You can add a setup.ini file to add command line switches, link in the transforms and point to patch files. You can modify the msi and transforms with the customization wizard. I don't recall if this is all documented, but I got the adobe customization wizard here http://www.adobe.com/support/downloads/product.jsp?product=1&platform=Windows
So my "Installation Program" is literally just "Setup.exe" and it automatically runs everything silently as long as the above ini files are in the proper content location.
Our environment is windows 7 x64 and windows 8 x64 so it definitely works from SCCM 2012 to those machines.
As they are MSI files, if SCCM says it's deployed then it should be - I suspect that there is some self repair/healing going on and it isn't completing for your user.
SCCM deploys in the system context, not the user context as your manual install would have been run in.
The logs will confirm this, or point you in the right direction.
Once you have a bit more informaiton on what is occurring post back and the community will try and help you futher.
I've installed lots of Acrobat across many clients with SCCM using the MSI and never had a problem regardless of the OS bit version. My guess is that the installation is attempting to finish the install with a user which does not have local admin rights. Login to a fresh install with an Admin ID to test.
If this is the case, you can add an Active Setup key to the transform file and have it launch a repair command. It'll leverage the local system account instead of the local user.