The first issue I am seeing is that the Install file command line switches I am putting into that field are not there if I save the XML and go back into it to edit it later. I'm almost 100% sure those commands stayed in that line in 9.1. I'm unable to go back in and edit those lines, and it also seems to be ignoring what I put in that line anyways.
The second issue I have is that it appears to be launching the patch file twice on custom patches.
My current example is a Visual Studio 2013 Update 5 patch I made.
I added the .exe to the deployment info tab, and when I deploy the patch I can go on the machine I'm testing with and that patch exe is running twice in the Task Manager. I let it sit for about 3 hours this morning to see if it would ever finish and it never did. I then decided to run the patch manually with a /passive switch to see if it would run manually and also to time the install. IT ran, and only one instance of the exe was in the Task Manager, the install completed in about 20 minutes.
I decided to try the /passive switch in the custom patch so I could monitor the deployment this time. Again the deployment launched 2 instances of the install exe and appeared to ignore the /passive command as nothing was displayed on the screen.
Any help would be appreciated.