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excelApp.Quit was the solution, doesn't even need the excelApp = Nothing, that actually screws it up more.

 

Here is the final code, works perfectly. Interestingly enough it still doesnt show the message box with the name of the document, closes it anyway. *shrug*

 

FileDIR = "C:\BOM Calculator\PART_BOM.xlsx"

excelApp = CreateObject("Excel.Application")
excelApp.Visible = True
excelApp.DisplayAlerts = False
	
excelWorkbook = excelApp.Workbooks.Add

excelApp.Columns.AutoFit  
excelWorkbook.SaveAs(FileDIR)
excelApp.Application.Visible = True
'Ask If You Want to Close Excel File
Question = MessageBox.Show("Close Excel File?", "Title", MessageBoxButtons.YesNo)

excelApp.Quit '<- THIS WAS REQUIRED
	
If Question = vbYes

	Try
		excelApp = GetObject(, "Excel.Application")
			For Each wb As Object In excelApp.workbooks
				MessageBox.Show(wb.fullname)
		        If UCase(wb.fullname) = UCase(FileDIR)
					wb.Save 
					wb.Close  
					excelApp.Quit
		        End If
		    Next
	Catch
	End Try
Else	
End If