Although you said you are using WRFv4.0, the rsl files indicate you're using v3.8.1, which is very old and not supported anymore.
Code:
taskid: 0 hostname: foghunter
module_io_quilt_old.F 2931 T
Ntasks in X 2 , ntasks in Y 5
Setting blank km_opt entries to domain #1 values.
--> The km_opt entry in the namelist.input is now max_domains.
Setting blank diff_opt entries to domain #1 values.
--> The diff_opt entry in the namelist.input is now max_domains.
Linear vertical interpolation is recommended with input vertical resolution this coarse, changing lagrange_order to 1
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REAL_EM V3.8.1 PREPROCESSOR
Can you please try the latest version - v4.6.1 - to make sure this is not a lingering issue from a bug in old code? Thanks!