You know sometimes scheduled agent(script) doesn't work as we expect but works fine when you select from the agent list. Also, no way to debug the scheduled agent. I also faced the same problem and I came up sending mail at regular intervals in my script ie. for every few lines I'll trigger a mail to my mail box with subject line as "Part 1", "Part 2", etc. By this way I can filter out the error part.
In your script(agent) add the following lines to trigger the mail
sub initialize
Dim oSession as New NotesSession
Dim oDb as NotesDatabase
Dim oDoc As NotesDocument
Set oDoc = New NotesDocument(oDb)
oDoc.Form = "Memo"
oDoc.From = oSession.CommonUserName
oDoc.Subject = "Part 1"
call oDoc.Send(False, "Your Name)
'Your script
.......................
.......................
.......................
oDoc.Subject = "Part 2"
call oDoc.Send(False, "Your Name)
.......................
.......................
.......................
oDoc.Subject = "Part 3"
call oDoc.Send(False, "Your Name)
.......................
.......................
.......................
oDoc.Subject = "Part 4"
call oDoc.Send(False, "Your Name)
end sub
This was first published in November 2000