demultiplexing in stacks gives empty files

One rad-seq plate runs demultiplexing fine, with the 4 output files ok. When I run the second plate for demultiplexing, no error comes out, but two of the output files come empty (orphan reads and demultiplexed samples) and I find the samples data in the hidden items, the problem is that I don´t know from where they come from, if from the orphan or from the demultiplexed. Any help on this?