Did you use CRA's AutoFill to import your tax information?
Yes. It downloads only proceeds and not costs of transactions, which need to be filled in by hand. The other way is much easier.
If you choose to report your Capital Gains using the T5008 slips imported from CRA, you need to go in and "Edit" each T5008 slip itself. When you import these slips from CRA, they are usually missing "Box 20", which is the "Adjusted Cost Base" (purchase price) of your shares. Without entering this number, you will have Capital Gains on the entire "Proceeds of Disposition".
You can choose either method to report these dispositions, but not both. If you've already downloaded these T5008 slips and wish to use to report them under your Capital Gains Profile, you need to "delete" each T5008 slip imported.
Yes this will fix it but entails deleting several hundred entries, I have a lot of investments. Using the Capital Gains Report only required 3 (three) entries. TurboTax should give you the option. Major design problem with this program.