1099-R box 7 Code 2 distribution amount not include in RMD calculations

I'm helping my sister who is 74 with her taxes, She has 3 IRA's and takes money from 2 of them to live on. The withdrawn amounts far exceed her RMD requirement. The one 1099-R has code 2 in Box 7.  I 2023, the same applied and the amount of withdrawal was included towards her RMD.  In 2024, the amount is excluded and only calculates off the one withdrawal and not both.  So when I add the information for the 3rd, the RMD amount calculated is short and a penalty is applied.  If I change the code to 7, normal distribution it calculates correctly. Has anyone experienced this and how to address it? Thanks in advance