Hi! I've got two sets of replicate (x3) HiC libraries. I think I've set the min.inward,  min.outward and max.frag thresholds for them correctly (or at least for the bulk of the datasets - not sure if I should set the threshold for replicate 3 individually?).

My question is: what is going on with these HiC libraries? Why do these peak heights look so different? Are any of the libraries "better" than the other ones? Are they usable?

Looks okay to me. You might want to trim your outward pairs at 100 kbp, just to get rid of the part where the red line is still above the blue line. I'm not sure what the enrichment of the same-strand (blue) pairs at a log-distance of 10-15 represents, my best guess is that it's a consequence of homologous pairing - I don't know whether that's biologically feasible, but this shouldn't really matter so long as it's not a technical artefact.

Anyway, I would proceed with the data analysis. The relative heights of the peaks aren't too problematic as long as you remove the inward and outward-facing reads. Yes, there will still be some systematic differences between libraries corresponding to the differences in the orientation profiles (probably resulting from differences in ligation/cross-linking efficiency), but as long as you normalize correctly later you should be fine.