Setting your white balance to "auto" or AWB lets the camera decide what the white balance will be. Taking the picture of your WhiBal card first and then setting custom white balance (CWB) to that picture lets YOU decide what the white balance will be. When taking pictures of your WhiBal card, you need it to fill nearly all or more of the frame. This is because setting a custom white balance takes an 'average' of the picture you tell it to. Note, however, that regardless of what you set in the camera as white balance, whether auto, daylight, shadow, custom, or any other value, it only affects the JPGs the camera produces...NOT the RAW pictures.
Since you took a picture of your WhiBal card and set that in your post program, (you did set the white balance to the RAW image, right?), what your post processing program should have come out right. But, from your initial post, I don't know whether you took a picture of the WhiBal card with the flash or without? White balance must be set to the identical lighting conditions the pictures are shot in. Shots without the flash and shots with the flash are two different white balance levels. I recently shot a family birthday party in a small banquet room at a restaurant that had a full wall of windows and cloudy-bright outside, with curtains open. I took 8 white balance shots...one in each direction, with and without flash, and then post processed all the pictures and set white balance by 'group' of where they were sitting and flash/no flash. There was still some minor 'tweaking' to do to get color consistency across all the pictures.
As for taking pictures of the WhiBal card with your flash, it's probably best to have someone volunteer to hold it and you take their picture...zoomed in such that the card is fills or nearly fills the frame. Then retrieve your card, go back to where you were, and take their picture. One nightmare I had to deal with was taking their picture with the flash with their back to the window. Their holding the WhiBal card effectively set the balance to how the flash was lighting their face. That's all I was looking for. As for the colors of the flowers that were lit from outside...they're close, but not right. I could have done separate white balance treatments on copies of the picture and then put them together, but I don't know how to do that yet.