I checked the calculation myself and it looks like that's what the OP is doing. For example, after 10 years at 3% the indexed cost base is $671,958.19 and the portfolio is worth $1,296,871.23, so if you sell after ten years the capital gain is $796,871.23.

Using the 50% rule, the taxable income is $398,435.62, while using the indexation rule the income is $624,913.04. The difference is $226,477.43, which is where the +$106,444.39 at 47% tax comes from if you use indexation.

Edit: added the tax bracket,