Have you tried removing all of your markings? You can always delete the markings in FeralHeart\\Textures and then re-fill it with the default FH markings found here. (http://www.feral-heart.com/index.php?option=com_jfusion&Itemid=2&jfile=index.php&topic=44252.msg611375#msg611375)
Then download the custom mass markings you want, place the markings.cfg into Local Disk (C:)\\FeralHeart and replace the original markings.cfg when asked. Don't forget to place the markings/textures into Local Disk (C:)\\FeralHeart\\Media\\Textures This time do not replace anything if asked.
If you're still having trouble, try opening the markings.cfg and re-arrange them a little if they seem out of place, or make sure that the listed default markings are at the very top of each section.
Well, sounds like you haven't placed the Markings.cfg into your main FeralHeart folder. That is what's needed in order for the markings to show up listed in-game. If there are only a few markings missing, then you need to add that to the list by adding them marking inside the .cfg file (open in notepad). Make sure it is set out like the others.
If there are still issues then feel free to ask for more help..
NOTE: This MAY be a cause, try everything else before doing this~
Well, if it asked you to replace your markings.cfg, then if the original markings weren't in that notepad, they were deleted. Whenever you download new markings, instead of replacing the markings.cfg file, just open the one you downloaded and copy everything new, pasting it in the right spot in your original markings.cfg file. Sounds like a lot, I know, but it's rather simple.
(http://i61BannedImageSite/zv28o6.png)
Here are the original body markings for the feline model. If I downloaded new markings, I'd copy everything under [FBody] from the downloaded file and paste it UNDER the [FBody] markings in your original file. This way it keeps everything you had, as well as adds all your new markings. Do the same with [Fhead] [Ftail] [Cbody] and so on~
If you have anymore troubles please don't hesitate to post. But for the time being, I'd re-download the default markings.cfg file and replace the one you have now with it. Then download the extra markings you wants and follow the steps above.
Here's the default markings file (just take out the .cfg file):http://www.mediafire.com/download/q5jd7h375675i4f/Default+Markings.zip (http://www.mediafire.com/download/q5jd7h375675i4f/Default+Markings.zip)