I'm having a similar problem. i AM running the .MSI, but that's what the documentation I read told me to do. I've created. I've created 16 packages and deployed 15 of them successfully by running the .MSI and then ExceptionDeployer.exe.
For whatever reason, InDesign is giving me fits.
UPDATE - it behaves the same whether I run the Setup.exe or the .MSI.
Here's what I think if the root of the problem from my PDApp file:
08/07/13 09:05:38:317 | [INFO] | | ASU | Setup | Setup | | | 1740 | TimeLog: End Installing. Now launching PDApp
08/07/13 09:05:38:832 | [INFO] | | ASU | Setup | Setup | | | 1740 | Deployment File Path not specified in command line arguments. Skipping payload deployment part
08/07/13 09:05:38:832 | [INFO] | | ASU | Setup | | | | 1740 | Event Guid generated is: 'c8075a56-f9a8-4989-a6bd-6cb14162f77f'
08/07/13 09:05:38:832 | [INFO] | | ASU | Setup | Setup | | | 1740 | ================= End Adobe Setup. Exit code: 0 =================
08/07/13 09:05:38:832 | [INFO] | | ASU | PIM | PIM | | | 1740 | PIMSqlite closeDB status 0
08/07/13 09:05:38:832 | [INFO] | | ASU | PIM | PIM | | | 1740 | FREE PIM Instance ...
08/07/13 09:05:38:832 | [INFO] | | ASU | Setup | | | | 1740 | Waiting for the async thread to get the task completed
08/07/13 09:05:38:847 | [INFO] | | ASU | Setup | | | | 3728 | Event with guid 'c8075a56-f9a8-4989-a6bd-6cb14162f77f' is being sent
08/07/13 09:05:38:878 | [INFO] | | ASU | Setup | | | | 3728 | GetIEProxyInfo - No default proxy present on the user machine
08/07/13 09:05:38:878 | [INFO] | | ASU | Setup | | | | 3728 | GetIEProxyInfo - proxy Url is
08/07/13 09:05:39:159 | [INFO] | | ASU | Setup | | | | 2160 | HTTP Request Status code 200.
08/07/13 09:05:39:159 | [INFO] | | ASU | Setup | | | | 3728 | The http request returned HTTP_Status:0 HttpCommunicator error:0
08/07/13 09:05:39:159 | [INFO] | | ASU | Setup | | | | 3728 | Async thread is completed. Now exiting from function.
08/07/13 09:05:39:409 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | Build Version - 1.2.0.4
08/07/13 09:05:39:409 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | Logging Level verbosity Set to 4
08/07/13 09:05:39:409 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | The return code from the Bootstrapper Process is (0).
08/07/13 09:05:39:409 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | Correcting Dependencies in local db.
08/07/13 09:05:39:877 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | STEP 4: Starting to launch Adobe Installer.
08/07/13 09:05:39:877 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | Obtained Adobe Common Folder Path.
08/07/13 09:05:39:877 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | Adobe Installer launch location is :: C:\Program Files (x86)\Common Files\Adobe\OOBE\PDApp\DECore\Setup.exe
08/07/13 09:05:39:877 | [INFO] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | deploymentFile = (C:\Users\jdoe\AppData\Local\Temp\{0EEF4A84-B390-492B-9226-3A77741E64 88}\\{90B1A10A-EDC5-45B7-B3C4-EC690B364DAA}), installSourcePath = (\\server\sandbox$\adobe\x86\InDesign CC x86\Build\Setup\Adobe InDesign CC_0)
08/07/13 09:05:51:748 | [INFO] | | ASU | DeploymentManager | AAMEEUtilities | | | 2108 | Process creation completed.
08/07/13 09:05:51:748 | [FATAL] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | The return code from the Adobe Installer Process is (26).Stopping the installation process.
08/07/13 09:05:51:748 | [ERROR] | | ASU | DeploymentManager | DeploymentManager | | | 2108 | Media Failed (Adobe InDesign CC_0)