Problem with silent instal of Imanage FileSite

I'm trying to create SCCM installation package which comprise of client side components of iManage Worksite Server. Package include following components FileSite, EMM, OffSite... My special requirement is to install them in "disabled state" so that user doesn't see presence of applications on his PC. We trying to pre-deploy this application onto users machines in such state and quicly activate it when users complete training.
I created package which in the end run VBS which disables appropriate addins in MS Office through which these apps integrate with Office. Packages run with admin user rights.
Initially it seems as fit for purpose solution, but after some testing following problem arise: for first time install as installation passes from administrative account, not from user account, after reboot active setup components writing user side settings (it looks like small pop up window with text "msiexex "APPGUID" /fu") and it somehow triggering these apps to enabled state... So in the result application became visible to users...
 
Any hint how to tackle this problem?

I don't know the software, but would it be possible to perhaps install it normally with ALLUSERS=2 and simply delete the shortcuts or ask it not to make any if such public property exists? and when you need the software, simply create links using xxmakelink ?

Thanks for hint, but seems this doesn't help in my case.
Let me be more specific about my problem. For example I'm trying to install FileSite 8.5, and I have a package which do it silently. This software integrates with Outlook and other MS Office through addins and I make a script which disables it (by changing Startup type of corresponding addins from 3 to 0) - it does what I need - disables program. I run it as a last step of my SCCM package. All rebuts are suppressed. But problem is that it adds following in Active Setup registry section:

[HKLM\SOFTWARE\Microsoft\Active Setup\Installed Components\{2C77E038-AB95-45E7-9B02-3D15A68D5464}]
"Version"="1"
"StubPath"="msiexec /fu {2C77E038-AB95-45E7-9B02-3D15A68D5464} /qn"

This cause run of msiexec /fu {2C77E038-AB95-45E7-9B02-3D15A68D5464} /qn after reboot for all users through the Active Setup mechanism. I don't know which user side setting it repairs / creates but apart from al other it change Office addins settings in HKLM section which I need to be disabled.
 
So I see 2 options:
1. Somehow run my disable script after reboot and "msiexec /fu {2C77E038-AB95-45E7-9B02-3D15A68D5464} /qn"... But I'm not sure how to do it better and for sure...
2. Kill Active Setup key - but here I'm not sure if it does something useful in terms of user side settings and either if it won't be somehow recreated upon reboot and will run anyway...
 

blog.danovich.com.au/2011/04/21/sccm-packages-waiting-to-install-package-installation-status/
 
Check this link out hope this will solve your problem...