I traced this problem and found something strange. When the child documents are loaded, after LoadLyxFile, updateLabels are called, and release a structureChanged() signal, which calls LyXView::updateToc() to update the Toc dialog (QToc::update()). It is strange to me that after the second child document is loaded, the signal does not trigger updateToc and lead to invalid iterators in the Toc dialog.... If you set breakpoints at LyXView::updateToc(), and updateLabels, you will see what I meant.
Still tracing... Bo