Actually it's the other way around. 5.1.4 has a bug which skips some files or packs them as 0 Kb files under some conditions. Akeeba Backup 5.2 doesn't. We already know what it is, it has to do with backing up large files across backup steps. This was broken in 5.1.x and fixed in 5.2.x. Try uninstalling Akeeba Backup and install 5.2.4 again.
FWIW PHP 5.4.9 is ancient. It MAY have bugs which cause PHP to report the wrong file size, leading Akeeba Backup to not backing up your files. This behaviour cannot be confirmed with PHP 5.4.45 so I will have to suggest that if this problem persists after reinstalling Akeeba Backup you should update PHP to something that's not obsolete and vulnerable, especially if you're running this on a production server.
Nicholas K. Dionysopoulos
Lead Developer and Director
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