Guys, I've just found a major problem. Fragmentation.
I was getting CTD on a file, then I went on the desfragmentation tool, ask for an analisys and on the report I saw that the file that was causing problems had 1.634 fragments!
Jesus Christ!
Some other files were very fragmented as well... What I did was, I removed the fragmented files to another partition, de-fragmented, and copied the files back over. Now they are all in only one fragment, no more CTD from that file.
I recomend you all to defragment the partition you are using for the sh3. Helps a lot on errors and loading times.