The NaN issue sounds similar to this one - and will hopefully have the same solution.
The merging of the b-values is trickier to address. Currently, volumes are grouped into shells if their b-values are within some tolerance of each other. Currently, this is hard-coded to 100 at this point in the code. The simplest fix is reduce that value to 50 or so. In the long run, we should make this a config file option - I’ll file an issue for that on GitHub.