Arduino Due not properly detecting SD card
Remove the caps please. Perhaps the scope itself creates the overshoot.

The Due is not special. It should work.

Can you tell what kind of SD memory cards and which SD module you use ?

Try the SD Formatter, see the post at the Arduino.cc forum: "Don't Format SD cards with OS utilities!".
Some SD memory cards are not compatible. Perhaps you have more luck with an older 1GB or 2Gb SD memory card.