Short version
Custom permissioning would seem to be applied (unexpectedly) via a WiX element or a custom action during the installation process (other possible causes discussed below - maybe check the major upgrade file revert possibility in particular - or the group policy possibility).
Clues for debugging can be found in the WiX source, or the compiled MSI file, or in a verbose log file (to name a few places to start). Details for each option below.
The below was written very "organically" - it evolved a bit - so it is a bit redundant. I will leave it as it is.
Other Possible Causes
Major upgrade file revert: It is quite odd that the file has less rights after the install. Perhaps this indicates a group policy or a file recreate during installation? The latter sounds very unlikely for such an important file - but it could happen if the update is a major upgrade and the original MSI installed the INI file as a file (instead of as INI file entries) and set it to be a non-permanent file.
In this scenario the INI file will be uninstalled and then reinstalled - likely stripping it of any custom ACL permissioning (ACL permissions are very complicated, they can inherit and override, and deny or grant, etc...). Any custom INI entries added to the old file will also be wiped out - check for such missing custom entries after installation.
This is a common problem (major upgrade file revert): major upgrade file uninstall and reinstall making the file appear reverted or overwritten when it has been wiped out and installed fresh instead and can trigger many other problems than ACL issues.
Other potential sources for the unexpected permissioning are also possible:
- repair / modify operation for another Lotus Notes-related MSI package targeting the same INI file?
- another MSI run as part of the same setup bundle doing permissioning?
- group policy / active directory processes enforcing standard ACLs? (sample)
- an executable / service run in admin mode doing something funky?
- scheduled tasks interference? (some possibilities)
- logon scripts doing something funky? (very unlikely in your case, but login scripts can do pretty much "anything" - and they do)
- some other, unexpected source. Something with admin rights does this - that is the obvious common denominator.
My 2 cents: if this is an in-house, corporate package, use group policy to apply permissioning instead and remove the operation from your package (unless you deploy to computers outside group policy control - but then you can have a special package which only does permissioning and keep permissioning out of your main package - making it less error prone).
ACLs
The problem you describe is very interesting. I am not aware of anything automatic in WiX that would meddle with ACLs, though I can not guarantee it. There are, however, constructs that are designed to change ACLs when you specify them explicitly - and you need to check your MSI for these constructs (described below)
But first of all: I ran a quick smoke test with a WiX MSI to see if I could replicate the problem, and I can not replicate it. My fear was that this could be something changed in a recent Windows Update. In other words some sort of security fix distributed without anyone's awareness which changes core functionality in Windows Installer (it wouldn't be the first one).
ACL-permissioning
Some info on how ACL permissioning can be implemented in your MSI. Essentially you can use ready-made WiX elements, or run your own custom action.
There are several WiX elements that deal with ACL-permissioning and they result either in settings added to standard, built-in MSI tables or they add entries to custom WiX tables. Look for these elements in your WiX source (if available) (samples):
I am not sure why the WiX guys decided to support all these different permissioning options - there are surely good reasons - since it must be a lot of work to maintain for them. I have written permissoning code myself, and in my view it is a time bomb of conspiratory complexity to deal with. Permissions permute like you wouldn't believe, but that is off topic here. In my condensed view very few permissions make any sense, but full flexibility is allowed by ACL permissioning - all the rope you need to shoot yourself in the foot. I prefer the generic "macros": GenericAll="yes", GenericExecute="yes", GenericRead="yes", GenericRead="no", etc...
Additionally you can use custom actions to call command line permissioning tools such as subinacl.exe, cacls.exe, xcacls.exe, icacls.exe or several other ones - which I would definitely not recommend for reliability and security reasons. Custom actions are never preferable when there are other options: Why is it a good idea to limit the use of custom actions in my WiX / MSI setups?
The Permission element I would not use for technical reasons, the built-in MsiLockPermissionsEx table I have never tested. The WiX-specific PermissionEx element is probably what I would choose to use if I needed this ACL permissioning at all.
Inspect MSI
If you have WiX source access, you should be able to find the permissioning elements or the custom action elements that cause the problem.
However, if you do not have WiX source access, you can also check your actual, compiled MSI file for any custom features that could apply custom permissioning. I would focus on the Custom Action table and any custom WiX / MSI tables found in the MSI in question.
In other words: inspect the compiled MSI file used for installation for custom actions and custom tables that are used to set ACLs. See MSDN for a list of standard MSI tables. Any table you don't find there is custom.
To inspect the MSI, use Orca or an equivalent tool. See this answer (towards bottom) for a list of tools you can use (commercial or free): How can I compare the content of two (or more) MSI files?
Verbose Logging
You can also do what I always do: create a proper, verbose log for the MSI install in question. This gives you something to start with to figure out what is happening - and as such it might in some cases be better than just inspecting the MSI. You can find some information on how to do logging here.
Alternatively, you can enable logging for all MSI installations. See installsite.org on logging (section "Globally for all setups on a machine") for how to do this. I prefer this default logging switched on for dev and test boxes, but it does affect installation performance and adds a lot of log files to the temp folder (that you can just zap once in a while). Typically you suddenly see an MSI error and you wish you had a log - now you can, always ready in %tmp%.
I would also make a note of what OS you are on, and determine if the problem is seen only on this OS? And this also involves figuring out if you have the latest hotfixes installed.
