The only empty folders in a new installation are:
/Data/Sites/1/index
/Data/Sites/1/systemfiles
/Data/Sites/1/SharedFiles
/Data/Sites/1/SharedFiles/History
However the Setup page code also checks for the existence of those folders and tries to create them if they do not exist. Only file system permission problems would prevent that.
You do have other working installations of the same version right? So that means there is nothing wrong with the package. Lots of people are using this version.
"Hosts can't find anything wrong with the .net framework either."
I don't know what that means. If the framework is not working as expected one should try re-installing it, doesn't sound like they want to try that. There is no one thing I know of to check for a funky installation of .NET but if it isn't working as it should it seems that is a good possibility that something is funky in the framework installation. The fact that it works everywhere else indicates some kind of problem in this specific hosting installation.
You could try installing version 2.3.9.3 to see if you get the same problems in this hosting.
Best,
Joe