When you send your withholding tax data and click on " receipt ", for all the cantons you get the total amount of what has been declared except for the cantons of Vaud and Geneva .

In fact, it displays a message asking the user to come back to the same place in 48 hours :

These are the only cantons where transmissions work both ways for the time being. Users are required to review their comments and take them into account.

48 hours after reporting, you have to go back to the transmitter log. Go to PUCS salary data export - journal :

Click on the receipt of the last withholding tax transmission:

Click on receipt :

On the right hand side of the receipt, there are messages from the  Tax Administration with their comments. As it is not very readable, it is better to save the receipt in text format.

Their communications can be of different kinds. Examples:

In this example, everything fits.

In this example, they ask to correct the municipality of taxation which they believe is wrong.

In this example, they do not agree with the scale applied.

In this example, something does not suit them but they do not say what in words... So you have to call them...