Library and sync problems

Hi, I'm using calibre with a Kindle PW and the Goodreads sync and reading list plugins with the following plugboard:

any format:KINDLE2 = ([{series:|| }{series_index:0>2s|[|] - }{title}] -> title)

This worked fine for a long time but now I find that some books are not showing in the library at all on the kindle (gaps in series) but if I search for the title they have actually been sync'd.

I've tried deleting everything from the kindle and a factory reset but the problem persists. Is it best to start from scratch with Calibre as well or is this a known issues?

I can't diagnose the problem to a specific plugin or setting without restarting but I'd rather avoid that if possible.

Thanks