Windows PowerShell Vs. SharePoint PowerShell for Deployments

The SharePoint 2010 Management Shell is an instance of PowerShell that already has the SharePoint PSSnapIn loaded. You can use either to deploy SharePoint .wsp solution packages.

Prefacing your script with:

if ((Get-PSSnapin "Microsoft.SharePoint.PowerShell" -ErrorAction SilentlyContinue) -eq $null)  {     Add-PSSnapin "Microsoft.SharePoint.PowerShell" } 

will ensure that it will run from either shell instance.

Source: http://sharepoint.stackexchange.com/questions/60230/windows-powershell-vs-sharepoint-powershell-for-deployments

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