I am using Excel 2007 interop assembly to automate Excel through c#. Interop version is 12.0. When I try to save a file, it can be saved only in 2003 format, but thats fine
Try instead workbook.CheckCompatibility = false;
I used the following in bold to make it skip the compatibility issue.
ActiveWorkbook.SaveAs Filename:= filepath or filename .xls" _ , FileFormat:=xlOpenXMLWorkbookMacroEnabled, CreateBackup:=False
Try ThisWorkBook.DoNotPromptForConvert = true
More info at DoNotPromptForConvert