Some questions come to mind:
Is this your only 3rd party custom app that you are deploying?
Of all the items you are deploying with Patch Manager, is this the only one giving you problems?
Is this the only one that requires the "custom custom" workaround?
(I have a few packages that are normally deployed with .vbs scripts that require admin privileges, but the only way to get it to deploy properly with PM is to use a temp.exe file that does absolutely nothing (just ignore the verify message), but allows me to upload all the other files and use a custom packageboot.xml that calls a CUSTOMNAME.cmd file in the post-execution section which has a single line of code: START /WAIT WScript "%~dp0SCRIPTNAME.vbs" //NoLogo)
Also, I have discovered when having these odd issues with PM, that sometimes, deleting the item from the WSUS server, and creating a whole new package helps - because simply making the changes in the package, and sending the updates to the same PackageID folder doesn't always work.
Hopefully, some of that info will be useful.
You have some great suggestions here; however, the issue is totally different.
The problem is that on "Select Package" screen, under Settings, Advanced, if "Install can request user input" is selected, somehow the context changes and the non-admin end user is prompted for Admin credentials.
I agree that deleting the package and creating the new one is always the best option. I am yet to have success in revising a file within a package. No matter how I try, the new file shows in the package, but not in the published package. "Package boot helper" file is worse. It displays the last used file instead of the one that is included with the package.
Exactly! Once you publish a package with content, unless you are changing the applicability or installed checking rules, any content change almost always requires a deletion then re-publish.
You may also want to keep a packageboot.xml file handy to overwrite every time you check that package boot helper option.
(also, make sure you delete the one that gets auto-populated, then when you click on the view .xml file - you will see yours)
Here's my generic that I use when I have to deploy a fake application that calls the vbs script (and as a when I need to create a new custom one)
<?xml version="1.0" encoding="utf-8"?>
<packageboot version="188.8.131.52" id="dd53b76e-babc-410f-8901-426d0989f5f1">
<process name="Application.exe" action="terminate" failureaction="stop" enabled="false" />
<program type="exe" typeaction="runandwait" name="TempPatch.EXE" successcode="0" failureaction="stop" enabled="false">
<program type="exe" typeaction="runandwait" name="CUSTOMNAME.cmd" successcode="0" failureaction="stop" enabled="true">
Please post if you actually get to the root cause and solution.