Hi Greg,
The jury is really out on all of this. We are in need of wet bench data, which is coming, but not here yet.
There is just no answer at this time. I ran a comparison of the different settings and the new setting will work for now.
An alternative when you run with the old settings is to parse the sequence into parts. I ran a 20kb length of a bigger genome and was able to run it at the previous setting easily.
All i have for right now. Will update with additional data. a;ways check the Bioinformatics Guide for latest settings because I will keep it updated.