FWIW, the lists of available dictionaries in the pull down of the spell checker is created from the available .v5dict files. In my tests, removing a .v5dict file from the \DICTS subdirectory removes that dictionary from the pull down list. Taking that a step further, I modified the content in a .v5dict file so that the entry for the dic and the aff file was invalid. This also caused that dictionary to not appear in the pull down list.
Based on these test results I think it would be worthwhile to compare the content of the .v5dict file of the Spanish dictionary with the content of the other .v5dict files to see if you can identify anything that is making them invalid.
The dictionary pull down list appears to be created during Pegasus Mail start up because changes made to the .v5dict files while Pegasus Mail was running were not seen until after it was restarted. It is probably a good idea to work on the .v5dict files with Pegasus Mail closed anyway.