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This is known behavior.
The first time the Sony reader opens the LRF file, if it does not already have it set up it creates some sort of page index. The Sony library software knows the algorithm that the Sony firmware uses, so it can create this index in advance. Calibre does not know the algorithm , so the reader has to create it when it first opens the book (and also if the first time you chagne to another font size while reading the book).
Regarding the sort by author in the GUI - that actually uses the author-sort field rather than the author field that is displayed. If you look at the metadata for the oddities you will almost certainly find that the author-sort field is not set up correctly.
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