Hi,
Which version of the card do you have? 512 MB or 2GB? What version of the firmware did you load on to it? The repair tool application is a glorified updater to 1.1.2 so I would keep that version on the cart until it's working. A few things to ensure:
Once you update/repair, format the partition in windows, then copy over the skin files.
Try putting in the cart in your DS and launching it, if it doesn't work, power it off and plug it back into your computer. Check to see if your data is corrupted (simply comparing MD5s would tell you). Finally if your data is in tact, it is possible the cart's contacts are not making a connection with the DS. I found it works better in a DS fat than a lite myself. So to make sure, cut out a small piece of paper the same size as the label and tape it on top of your label for the DSX and try it then. It might magically work.