First, ModeloEstandar welcome to MobileRead.

Glad to have you here.
Second, the PDFLRF application igorsk mentioned above is the best that I have used for converting both PDF and DJVU files for use on the Sony. (It also works on CBR, Comic Book archives.)
Third, it does seem odd that only a few of the files are being seen by the Sony. I can offer no additional solutions at the moment other than to try the internal memory of the Sony and see if they are seen. (Sorry about that turn of phrase.)