Initially I just extracted everything from the original WAD files we were using as BMP files, then Janis added support for PNG images, so I just simply converted everything to PNG with PSP 9, this problem appeared. After that, missing sprites were discovered in the PK3 file (which were also missing from the WAD files <!-- s:P --><img src="{SMILIES_PATH}/orc4.gif" alt=":P" title="Razz" /><!-- s:P -->), then I found an utility called UNWAD that allowed to extract every resource from a WAD file and insert it inside PK3 files, so I used it to extract Hexen and Heretic sprites, the tool extracts PNG images as the ones I described (with alpha channels), but the rest of the stuff remained the same, thus displaying with cyan pixels.
Yesterday I extracted the Doom resources and imported them to the PK3 file, they now look properly, but the new sprites can't be extracted like that, so they must be fixed by hand (which I'm doing now <!-- s;) --><img src="{SMILIES_PATH}/orc9.gif" alt=";)" title="Wink" /><!-- s;) -->), hopefully knowing this will allow me to work with the correct format to avoid problems like this one in the future <!-- s:D --><img src="{SMILIES_PATH}/orc6.gif" alt=":D" title="Very Happy" /><!-- s:D -->.