Hi Nicholas and welcome to the forum.
I can't recall ever hearing that one before although I seem to recall a report of the last line of reports missing sometimes from certain report creation applications which were not fully indicating an end of file.
That said this does not seem to be your situation.
Is the report just opened without a model applied when the lines go missing?
Is the file something that can be shared with others? Monarch Technical Support might be able to provide analysis or a few of us here on the forum might be interested to investigate and assess where the problem might be.
I've seen this with some big SAP reports, especially around page breaks. Sometimes you can fix this sort of behaviour by going to the Options menu, selecting the Input dialog, and ticking combinations of "Ignore Form Feed Character" and "Ignore unused print control characters".
You could also try saving a new copy of the report from Wordpad (make sure you save it as a text file), as that might get rid of the gremlins.