I had many of these same problems for a while. My problem turned out to involve a buggy SD card reader on my laptop. My suggestion is, first, to try a different card reader (a USB reader worked for me), then download and install the program from this link:
http://panasonic.jp/support/global/cs/s ... atter.html
After installing, run it and select the OPTION button, set FORMAT TYPE to FULL (ERASE OFF) and FORMAT SIZE ADJUSTMENT to ON (for v. large cards). This is the best way to format an SD card; the Windows format utility doesn't always format it properly to the SD card specification. This procedure fixed some very strange problems I had with an SD card, where a Windows format card caused the SD card to lose some of its capacity, and resulted in the "erased" files still showing up in the Wii save manager!
Even after this, sometimes I've noticed that the Wii will still refuse to see the Twilight Hack, but I think there is a different cause for this. If this happens with you, try copying it over again, or copying over a Zelda save and overwriting it with the Hack.
In any case, if you insert an SD card that reads fine in your Wii into your computer and Windows reports that it's not formatted and offers to format it, do NOT take it up on its offer! Instead, use a different card reader.