[Quoth]

I bought 200 Years to Christmas by J. T. McIntosh via Kobo, though it's on Amazon too.

Part of the Gateway SF essentials republishing with boring yellow covers.

Two main issues:
1. The small caps lead-in (start of every chapter) was about 0.45em of same font making it hard to read. Changed that to 0.85em rather than experimenting with real small caps or removing it because the source was ALL CAPS. I've seen that often.

2. Each chapter progress was reported as the entire book progress! Never seen that. It passed the Ladybird/Ladybug icon epub check, but on the green box epub check there were two ToC related errors I 'd not seen before. One was some sort of syntax, so I removed a property from the tag and that went away. I didn't understand the other to do with page-map

So I thought, I'll use the Edit ToC tool. As usual it had a couple of pointless entries, so I deleted and hit save. Error gone away.

I looked at the files again and there was a page-map.xml and it was in the manifest, but since the ToC was edited slightly, no longer actually used anywhere. So commented out the manifest entry and everything still OK. Removed the page-map.xml file.

Deleted and resent saved epub to Kobo ereader after a check in the Calibre viewer. Now book progress is properly reported. System ToC still works (it was working at the start).

So a weird error in a big publisher's epub, but easily fixed in Calibre.

Mostly weird stuff happens when people try to be too clever. Fortunately the actual files seem to be in the correct order. Most ereaders can only sanely do sequential files.