The value displayed in the controller window is the daily rain value from your console, the value in the NOAA report is the calculated value for the day.
Where there is a difference, it's normally an indication that sometime during the day your daily rain fell to 0 then went back to its previous value.
WeatherCat calculates rain over a period by adding up the differences between samples. Your daily rain should be slowly increasing throughout the day as it rains. If it drops, then comes back up, this will effectively double your rain - for example, if the rain is:
0mm, 2.0mm, 2.0mm, 2.0mm, 0mm, 2.0mm
across that period WeatherCat will see 4mm's.
To correct this, open the data editor and scroll down the raw rain column looking for a drop in the value to 0 followed by it going back up in subsequent samples. Edit the 0 to the previous sample value then reboot WeatherCat - they will then agree.
The last one of these I saw, the problem was occurring because the computer was going to sleep, which was causing a valid record to come in but with a rainfall of 0, which then picked back up on subsequent samples.