If there is an individual fixel with a value of ~3000 in the null_contributions file, that would be the first point of interest. See some explanation here. Even if your Z-statistics seem reasonable, there could be one fixel that is generating massive enhanced statistics, producing a null distribution with very large values and therefore making it impossible for any fixels in the empirical data to exceed that null distribution. The question is where that fixel is, and why it is repeatedly generating maximal values across such a large fraction of shuffles. The situation where I’ve observed this myself is when you have a fixel that does not have any streamlines connectivity, which is why as of 3.0.0 there is sometimes a warning issued about such fixels being excluded from testing. If you’ve already masked out such fixels, then maybe you’ve found some mechanism by which this problem can arise that I’ve not myself yet seen.
See what you can find by navigating through your raw data; if you can’t find anything I can have a look, but I’d need access to all of the inputs used for the fixelcfestats call.