I have come across a problem when trying to simulate wheat yields using DSSAT3.5 for a growing season that spans from 1999-2000. The model only includes the scheduled irrigations for 1999, but misses the ones for 2000. If I change the WHX file to run the same experiment but from 1998-1999,  or from 2000-2001, then it uses all the irrigations correctly.

Has anyone else seen this, and if so found a solution?