@shmish Box 16 on T4 is Employee's CPP contributions. Box 16A is Employees’ second CPP contributions.
This is not a software issue, because if you have a 2nd contribution (box 16A), you should logically have a 1st contribution (box 16). Technically, both amount should be on the same T4.
As suggest by @Leonard02 , if the last version of your T4 on your CRA My Account is not with box 16 and box 16A on the same slip, we suggest you to contact CRA to see if you can combine both T4s together to have only 1 but with all the amount reflecting your 2024 year.
Here is the link to contact CRA
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