I don't see how this can be blamed on fnv1a
Oh the irony :-) It turns out that it is in fact due to fnv1a. I reverted to 1438 and just added the fnv1a hashing algorithm to it to reproduce the issue. It took some effort to narrow it down, and some performance profiling.
The older hashing algorithm distributes data unevenly across buckets in the hash table, so some buckets have far fewer/greater items in them than others, however it is distributing individual items better. At least, with certain combinations of data. With some combinations of data, it leaves many buckets empty.
The fnv1a algorithm distributes items more evenly across all buckets, however, due to its lack of avalanching, more similar items are being stored in the same buckets. This means that when a hash matches a bucket and it has to be searched, even though there are fewer items in it (because they're more evenly distributed across buckets), the string comparison call takes longer as it is matching more characters per item because they are more similar, even though there are fewer string comparisons.
Unfortunately, every other hashing algorithm I have tried, eg. murmur3, xxhfast32, lookup3, takes more time to create the hash, at least for short strings. So it looks like we may just have to stick with the older algorithm.