Here are the results for running the ANOLEA assessment on the two templates: 1it2B and 1ux9A:
Given the high quality of both of the two template structures as judged by ANOLEA, it seems that differences in the qualities of the models are likely to be real - i.e. the second model (built from the lower resolution 1ux9A template) is likely to be of poorer quality that the first model (built from the higher resolution 1it2B template).