Followup on my problem from before: I still haven't managed to fix it so the NatBib and apalike Bib style work happily together. I've changed to an alternative style (simple natbib essentially) and it seems to work OK. Because this works fine, I assume that it is something weird about the apalike style once you get to more than 30 citations, or to having more than a couple of articles by the same author.
Hope that reassures anyone who's stressed about it happening to THEIR thesis ;-) Still very little clue about how to fix the original problem, but I think it needs someone with more LyX/LaTeX knowledge than me and the time to look (my diss is due in 4 days!!) Thanks Meri -- "Because it's not *always* the quiet ones" <shameless plug> http://blog.meriwilliams.com/ </shameless plug>