I've reset to defaults, tried different RAW converters. I did notice that Helicon Focus was showing 100% view magnification but the image displayed in the preview window was tiny so I suspect there is something wrong with the RAW filter handling now.
Program version V5.3.11 x64, all images shot using Canon 6D and helicon remote.
(edit: Just tried a set of shots from my old 50D, RAW format, taken long ago and definitely worked before, and they too produce the same error).
(edit 2: Installed Beta v6 which doesn't cause the file anomaly error but now images are purple tinge, indicative of the dynamic range being crushed. I've seen that behaviour in incorrect RAW conversions with other programs)