Hi Steve,
I really wish I could help but from my own experience, I've not come across this problem.

I have had to import data three times over the years and each time I used BigDump. It has its own peculiarities but it has worked for me each time.

Can we take it that your problem is now resolved? I guess you just want to resolve this to future-proof your imports?

Perhaps you could try importing with BigDump on a test server?