Since PDF2XL Enterprise accommodates silent conversion, you can run it as a scheduled task in the background.
It's important to understand that, while we do support our software, we are limited to the assistance we can provide for Windows settings. This is not something that should be attempted if you are unfamiliar with setting up Windows Scheduled Tasks, as we will not be able to guide you.
In order to create a scheduled background task, you need to use the Windows Task Manager to create the task and use a standard command line.
You may want to include a call to move the processed files out of the folder to avoid reprocessing them.
for /F "delims=." %%g in ('dir /b "c:\Input"\*.pdf') do "C:\Cogniview\Development\PDF2XL\Debug CLI\PDF2XL.EXE" -input="c:\Input\%%g.pdf" -layout="C:\Layout\test.layoutx" -format=excelfile -range=all -output="c:\Output\%%g.xls" -noui -autoopen=off & move "c:\Input\%%g.pdf" "c:\Converted\"
Once that has been done, it's vital to make sure that the Excel program is working with the system (or non-interactive) user. If it isn't properly set up, the output will fail to process.
Since this is an Excel-specific issue, we cannot assist with ensuring your system is correctly set up.