The IDAY variable in the MODTRAN tape5 file (appears in both Card 3ALT and Card 3A1) serves two purposes: (1) it is used with the time to position the Sun when MODTRAN's built-in ephemeris model is used and (2) it is used to determine the Earth to Sun distance, which impacts the exo-atmospheric irradiance from the Sun.
As part of the modifications made to the template tape5 file, make_adb switches the template tape5 file to always use an explicitly defined solar or lunar geometry (based on the DE405 ephemeris model built-in to DIRSIG itself), which insures that the thermal model (THERM) and MODTRAN are using the exact same position. That eliminates one of the purposes of using IDAY (the sun position) but not the need to have it for the Earth-Sun distance. It was observed that the IDAY variable was correctly set for Card 3ALT runs (used for the solar and lunar irradiance) but not for the Card 3A1 runs (path and sky radiance). For those runs, the IDAY variable was left unchanged from what was in the template tape5 file.
The code to update the IDAY variable in Card 3A1 was added. This change will appear in the 4.7.x release cycle.