MSBuild command line vs. Visual Studio publish

I have a solution with multiple projects, from which one is a web application of that I want to create deployment package. When publishing with Visual Studio, it publishes and deploys without any problems.
Due to some requirements, however, I need to publish it with command line and this is where I am having problems. Publishing alone works fine even in command line, but when I try to deploy package created in command line I get this error:

A value for the 'setAclUser' setting must be specified when the 'setAcl' provider is used with a physical path.

My msbuild command looks like this:

msbuild Solution.sln /p:DeployOnBuild=true /p:PublishProfile=Debug

One differences I noticed are that when publishing solution, PackageTemp folder is created in different projects and so when deploying it is printing different paths to cmd. With VS publish they look something like

"Default Web Site/MySite/..."

but with command line publish they look like this

"C:MySolutionProject(only a library project, not the one I want to publish)objDebugPackagePackageTemp..."

Thanks for any help

Edit: Created .zip packages are almost the same, except for archive.xml which has some different values and I suspect this to be the problem, but unfortunately I can't make any sense of what does this file actually represent.

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