SCCM 2012: Problems deploying x86 software on x64 systems
Community Chosen Answer
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.