By design there is no such limitation. I just tried with about 61000 files (57GB) and it found them all without problems. Maybe your backup set has some rules that filter out some files? You can e-mail your system info from Backup Magic editor (Help | Copy System Info) along with your backup set file. If everything looks OK in backup set file, try looking at what folder it stops, maybe this folder has too many subfolders or some other anomalies that may cause the program to misbehave.