Canon Rebel xt does not accept CF cards for no apparent reason

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Err 99 could means several different things, such as... Memory Card, Lens or Lens contacts....

Here's what you can try:
Remove the memory card an enable "shooting with out memory card" and see if you still get the error. If it works your memory card is bad. Try another lens if you can. Clean the lens contacts with a pencil eraser (be careful not to get eraser dust in the camera body or in the lens). Worst case scenario is, Err 99 could be related to the shutter failing which would mean a trip to Canon.
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mine has done this to me before.

dump all of your photos on to your computer
put the card back in the camera
in playback mode, hit the menu button.
in the menu, scroll over to the first settings tab.
there should be a "format" option.
Format your card.
this *should* fix it.

Have you tried formatting the new cards in the camera before trying to use them?

Check the pins inside the card chamber...is one of them bent?

1. Test the CF card on your computer or another camera. If it works fine then it may not be the card. Make sure the card is not UDMA, 4GB or more in memory size since those new big cards are not compatible with the older cameras.
   
2. Look inside the CF port. Make sure that none of the contacts that connect the camera and CF card are bend of smashed flat. If so then the camera will have to be send off for repair. This is a rather expensive repair, $250 is not uncommon.
3. I it is neither of these then take the camera to a local camera shop and ask them to look at it. It may need to be sent off, but testing another brand card, or resetting the camera or checking for physical defects couldn't hurt at this point.
   

Joe, this happened to me, just tonight... I got a new CF card and stuck it in, turned it on and one CF card flash. Completely dead from there. I found one of the CF card pins bent over, shorted out the socket and blew the mainboard fuse. I took the camera apart, found the fuse (labelled K) about under the set button area) I bridged the fuse with a bit of solder, straightened out the pin in the socket, put it all back together and it's working fine. The fuse is under the right side shield cover, it's labelled with a letter K. There is another fuse on the power inlet board (below the shutter button) and it's labelled 'P'...

1st, make sure the camera is in the Creative zone P, TV, AV, M or A-Dep. I have made this mistake many time and everytime I forget I moved the dial.

If dial is in the Creative Zone and still no RAW option then have the camera format the card, if that doesn't work do the following:

Turn off camera,
Remove lens,
Put on body cap.
Remove CF Card
Remove Battery
Let sit for about 30 minutes.
Put battery back in.
Put CF Card back in
Turn camera on
Put camera in Creative Zone
Push Menu button
Push Set button twice and check if RAW is now an option

If not then you can try the clear all settings function in the Set-Up 2 menu. Push the menu button then the left arrow button arrow down to the clear settings line push set the clear all functions.

If this doesn't help then I would say carry it to your nearest Canon Dealer that offers cleaning and service.

You've probably gotten bent pins in the camera. Has to go to the shop.

According to Canon, Error code 02 means that "There is a problem with the CF card. Try any of the following: Remove and re-insert the CF card. Format the CF card, use a different CF card."

Are both CF cards the same brand? Sometimes some brands have conflicts with the camera, you might try using two different brands.

It may not be the card, did you try on the third attempt to remove the battery and put it back in? There may be a problem with the contact points where the CF card plugs into the camera, or in the transfer system itself.

Change out the CR2016 3V battery. You have to remove the rechargeable battery to get to the CR2016. Refer to the manual for proper instructions.

Had the same issue with a two year old camera. This solved my problem.