Yup, orphaned video files are the cause. I complained to the developer about this issue 2 months ago when I found it had affected one of my systems. What BI version were you running?
Another symptom is you'll see a lot of "Clip: Disk full" in
Blue Iris's log, and occasionally a "Move:" or "Delete:" line logged showing a small amount of data being moved or deleted (depends on your storage configuration) and on the same log line typically it will say you have a very small amount of free space (e.g. "20K free"). What this boils down to is that Blue Iris sometimes forgets it owns some of the video files, so it does not consider them to be part of its allocated space anymore and it will not automatically delete them. Eventually enough of these orphaned video files accumulate that they use all or nearly all of your unallocated free space, and there is no longer enough space on the disk to sustain continuous recording between automatic maintenance cycles. Because things are so out of whack, the automatic maintenance deletes too few clips so the disk fills up again before the next maintenance cycle.