You didn't mention how you are processing....
Writing Command Line? Are you giving enough time between each file process?
Have you tried processing an .xprj rather than seperate files?
Writing VB? Do you close Monarch after each file process?
When you get this message, do you check to see if Monarch is still running in the background (via Task Manager)?
You could run code to create a file that is actually a linked table in Access (i.e. a .dbf or a .asc file
Here's code I run for most automated monarch processes I have in Access. I have the code attached to the On-Click event of a command button called ImportDailyRecords.
Private Sub cmdImportDailyRecords_Click()
Dim MonarchObj As Object
Set MonarchObj = CreateObject("Monarch32")
MonarchObj.SetProjectFile ("G:GROUPSEVERYONEDaniProject Name.xprj")
MonarchObj.ExportTable ("G:GROUPSEVERYONEDaniOutput table name.dbf")
Set MonarchObj = Nothing