Try changing your command line to this: (perhaps powershell.exe isn't in your path variable?)
%windir%\System32\WindowsPowerShell\v1.0\powershell.exe -ExecutionPolicy ByPass "%SCRIPTROOT%\RemoveApps.ps1"
Also, check your boot image, if this is running in WinPE, make sure you've enable PowerShell in your Boot Image. Perhaps the "File not found" is referring to your PowerShell.exe