I ran into the same problem and was told it was because AAMEE packages files for distribution using SCCM and ARD. To get around this issue, we created a self-extracting zip file containing a batch file to start the installation. I am sure there was probably a better way to accomplish the task, but this is what worked for us based on system restrictions and server permissions.
Batch file contains the following text: (Modify echo text as you see fit and include your msi filename in the msiexec line)
echo "Press ENTER to begin installation."
msiexec /i Build\YOUR_MSI_FILENAME_HERE.msi
Exceptions\ExceptionDeployer.exe --workflow=install --mode=post
echo "Press ENTER to exit installation."
You might want to change your user name to avoid getting spam.
I look into the various information from Adobe's forum and I find this usefull video :
After that I tried another thing just to be sure.
When you create your MSI package, during the "Configuration" page, select "Ignore conflicts and continue installation".
Before using SCCM to deploy this MSI, I tried locally from a command prompt (run as)
msiexec /i AdobePhotoshopCS6.msi (without any parameter) to view the installation progress.
At the end it works fine and the software has been installed properly.
Now il will be able to try through SCCM.
I would add, that the MSI package created with AAMEE can be used with SCCM or any other tool that can push/upload the package (folder container).
SCCM is a basic tool that upload the package to the destination (WS), once done, a command line (or batch file) will be ran from the WS.