ive had a 64gb card in the evo lte 4g since launch. no issues at all.
you may have some read/write errors on the card that need to be addressed.
if you can put the card in a computer, can you see EVERYTHING on the card? if so, copy everything off the card on to the computer. i use a pc , so if you are on a mac, use the utility that does the same thing as the utility within windows that allows the computer to scan the card for errors and fix them.
so, making a backup as described above, just make an image of your card and copy it to the computer.
then do the scan disk utility to fix any errors.
after that is done, just put the card back into the phone WITHOUT copying over the image you made earlier. see if you are able to access te contents on the card and use it normally.
if you are still not able to use it normally, then you will need to reform the card in the phone. then copy over your image you made and you should be good to go.
this occurred a lot on the original evo 4g and i think to some extent on the 3D with 32gb cards.
also, the brand of the card (speed is not a factor as the bottleneck occurs in the phone so having a certain class of card is not as important here) is a little important. for me, ive only used sandisk and i have not had those issues. there are even fake sandisk card on the net so be careful.
are you rooted? latest jb updates and all that?