That is how it should be.
Is that a 64-bit server and if yes do you start the 32-bit or the 64-bit powercli prompt ?
When you start the PowerCLI prompt, the PowerCLI should already have been loaded.
Which the working Connect-VIServer confirms.
Can you check in any case with
Get-PSSnapin | Select Name
Does the script do anything when you put just a regular PowerShell cmdlet in there ?
Something like Get_process for example.