In the latest version 519, average and diagnostic files are indeed generated and no errors occur. However, those files do not contain 3D and 4D variables such as 'ubar_bstr' or 'salt_rate'. They only contain 1D and 2D variables like 's_w' and 'x_rho'. All variables in history files are written normally.
I do not have a fix, but one difference between the two versions is in wrt_diags.F In the latest version, there are lines like this (line 92) before the variables are written:
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IF (Dout(ifield,ng)) THEN