That would make sense. My inline TOC has always been a separate (x)html file. Which would explain why I've never experienced the problem myself.
The official "documentation" is not exactly crystal clear here (or anywhere really), but section 3.3.2 (TOC guideline #2) of the Amazon Kindle Publishing Guidelines
does start with; "Place an HTML page
with a table of contents at the beginning of the book". Perhaps it should be taken literally. More evidence that the single-html-file source approach is going the way of the dodo.