FYI: Same problem with running on a build server (Jenkins with msbuild 15 installed, driven from VS 2017 on a .NET Core 2.1 web project).
In my case it was the use of the "publish" target with msbuild that ignored the profile.
So my msbuild command started with:
msbuild /t:restore;build;publish
This correctly triggerred the publish process, but no combination or variation of "/p:PublishProfile=FolderProfile" ever worked to select the profile I wanted to use ("FolderProfile").
When I stopped using the publish target:
msbuild /t:restore;build /p:DeployOnBuild=true /p:PublishProfile=FolderProfile
I (foolishly) thought that it would make no difference, but as soon as I used the DeployOnBuild switch it correctly picked up the profile.