Job is skipping PI message processing

Hi Gurus,
I nedd help in our PI message processing. Here is our issue:
Everyday there is a batch job in SM37 (a customized program for all 3rd parties that is connected to PI) that retrieves the daily files from the 3rd parties systems and these are then pulled from the 3rd parties system onto our repository and it passes the file to the ISU system (The communication channel opens up (triggers the upload of the file) at the end of business day and then grabs the file and this file is then processed through PI and also then moved to the archive folder).
This part is currently working as it always has. Normally in PI SXMB_MONI we then have reference to the file being processed through PI. This is NOT currently occuring in PI. When this script executes (for the past 10 days) there is no reference in PI in relation to the file being processed through, it simply has no traceability of this file ever being processed through. The files are being transferred as expected, but there are no messages being generated for reference.
What is extremely weird is the fact that when we manually complete this process it works with PI as it has been procesed/moved through PI. The only difference I think is the processing of the script is done in background and when we manually reprocess it, it is being executed in foreground. BUT, then again, this just happened abruptly. We did not have any system changes.
There are no errors being generated by the system. Am I missing something here? This has just happened so sudden.
Please help. This has been affecting our business for quite some time now (more than a week).

Dear Madelynne,
may I ask you to provide some details on this scenario:
(1) Is it an synchronous or an asynchronous scenario?
(2) Do you see the messages showing up in monitor of AdapterFramework?
(3) Do you see messages of other scenarios in SXMB_MONI?
Best regards,
Harald Keimer
XI Development Support
SAP AG, Walldorf

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