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This problem has been fixed and is available in the SeaDAS 5.1 Update 06 (and MODISL1DB 1.4.1).
The update fixes a problem in the MOD_PRO2 (terra_l1bgen) processing code that was causing MODIS-Terra L1A to L1B processing to fail depending on which calibration LUT versions were being used. The issue was determined (by MODAPS and the OBPG) to involve the RVS correction limits set in the PreprocessP.h file. The threshold values have been relaxed in the PreprocessP.h header file from:
#define RVS_CORRECTION_UPPER_LIMIT 1.2e+0
#define RVS_CORRECTION_LOWER_LIMIT 8.0e-1
#define RVS_CORRECTION_UPPER_LIMIT 2.4e+0
#define RVS_CORRECTION_LOWER_LIMIT 4.0e-1
This change appears to fix the problem. The new terra_l1bgen binary should now work with any past and future calibration LUTs.