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We are well beyond my understanding of the relax code (and I haven’t been able to get the relax people interested in it). It may be that fix_residues_to_native only works with abrelax, and not regular relax, I am not sure.
I don’t see a command line flag for relax that appears to affect constraint weights other than the ramping one. The variable name for the ramping one implies it ramps down, not up. You may be able to turn ramping OFF and alter line 396 of RelaxProtocolBase.cc to set the coordinate constraint weight as high as you like.
I second jtmacd that zero occupancies are a likely culprit.