Thanks for the edits above!
I can see how that example might have spooked you! The layout of that example isn't great, and doesn't apply to your situation as you were over the threshold at the time of both benefits whereas that example had unused threshold for the second benefit.
The proper layout where there were prior benefits is per the following 6 steps:
1. Group Threshold =€335,000
2. Taxable Value Prior Benefits = €397,000
3. Unused Portion of Threshold = Nil
4. Taxable Value of Current Benefit within same Group Threshold = €46,000
5. Taxable Excess on Current Benefits = €46,000
6. Tax on Current Benefit = €15,180
If you go back to the example and plug in the numbers following the steps above, you will get the same answer as the example.
Revenue's Guide to Completing the IT38 can be found
here and the methodology above can be found on Page 26 (Example 3).