Customers may experience two error messages at the beginning of an executed package (please see screen shot below for an example).
The issue is caused by Microsoft is loading and executing the packages within SQL Server Data Tools. SSDT for SSIS 2014 & 2012 incorrectly load the package without initializing the project causing these errors to happen. SSDT for SSIS 2016 has resolved this issue and loads the project context before initializing the package and these errors do not occur.
To demonstrate the issue, a test project was created. The project is very basic with three (3) blank packages. None of the packages use Pragmatic Works Audit Framework.
(A) One package without any logging.
(B) One package with logging enabled that uses a package-level connection manager.
(C) One package with logging enabled that uses a project-level connection manager.
The package without any logging (package A) and the package with package-level logging (package B) execute without any errors. However, the package that uses a project-level connection (package C) throws the error indicating that it can't find the project level connection but still completes with success.
These packages are extremely basic, blank packages that do not have any frameworks applied to them, and the behavior illustrated is due to a Microsoft issue and not a Pragmatic Works issue.
Customer(s) should note that this this issue has been resolved by Microsoft when using SSDT 2015.