run_tower --ad flag not working correctly
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Description
### Brief summary of bug
following instructions in [this NEON tutorial](https://github.com/NCAR/CTSM-Tutorial/blob/EMBER_Tutorial_2025/notebooks/ProjectExamples/customizeCase_spinupExample.ipynb) to create an AD NEON case my case only ran for 5 days. This makes me wonder if other user_mods or features of the run_tower command are also broken.
Note I was doing this in the cloud, for a tutorial, but I'd expect the same behavior on Derecho.
using ctsm5.3.043
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