OK after walking away from the problem for a little while, a little more coffee and applying some logic. I got the thing to work. So just in case you need a script to do what I was after and run a specific macro on a specific worksheet in the same workbook, here it is.
$excel = new-object -comobject excel.application
$excelFiles = Get-ChildItem -Path C:\Test\Daily_update.xlsm
$Date = (Get-Date -Format dd-MM-yy)
$workbook = $excel.workbooks.open($excelfiles.fullname)
$WS2 = $workbook.worksheets.item(2)
$WS2.Activate()
$excel.Run("Test_Refresh")
$WS3 = $workbook.worksheets.item(3)
$WS3.Activate()
$excel.Run("test_Refresh_2")
$WS4 = $workbook.worksheets.item(4)
$WS4.Activate()
$excel.Run("test_Refresh_3")
$workbook.saveas("C:\Test\SQL\Daily_update_$Date.xlsm")
$workbook.close()
$excel.quit()
Just to add a little more to this. After some trial and error I found that the following code was far more efficient at running than the above. Also I noticed that if there were only 3 worksheets it was fine but any more started to raise errors, especially when calling sheets. But this problem disappeared when the workbook was opened and visible.
#Call the application
$excel = new-object -comobject excel.application
#Now we select the file and path
$excelFiles = Get-ChildItem -Path "\\Server\Test\Daily_refresh.xlsm"
#The next variable speeds the script up by not calling the comobject as often
$app = $excel.Application
#Get system date and time and format it to comply with the final filename format
$Date = (Get-Date -Format dd-MM-yy)
#And again for the year folder
$Year = (Get-Date -Format yyyy)
#Test if folder exists
$DestYearFolder = "\\Server\Test\Daily_Refresh_Output\Test\$Year"
if (!(Test-Path -path $DestYearFolder)) {New-Item $DestYearFolder -Type Directory}
#Same as above only for the month folder
$Month = (Get-Date -Format MMM)
#Test if folder exists
$DestMonthFolder = "\\Server\Test\Daily_Refresh_Output\Test\$Year\$Month"
if (!(Test-Path -path $DestMonthFolder)) {New-Item $DestMonthFolder -Type Directory}
#Now we open the Excel file and activate the macro enabled content
$workbook = $app.workbooks.open($excelfiles)
#The next command makes Excel visible
$app.Visible = $true
$workbook.Activate()
#Now we run all the Macros that need to be run.
$app.Run("Macro_1")
$app.Run("Macro_2")
$app.Run("Macro_3")
$app.Run("Macro_4")
$app.Run("Macro_5")
$app.Run("Macro_6")
$app.Run("Macro_7")
$app.Run("Macro_8")
$app.Run("Macro_9")
$app.Run("Macro_10")
#Now we save the workbook in the standard daily format and the close Excel
$workbook.saveas("\\Server\Test\Daily_Refresh_Output\Test\$Year\$Month\Daily_Refresh_test_$Date.xlsm")
$workbook.close()
$excel.quit()