Cuffdiff and Cuffmerge problem

I ran Cuffdiff on paired-end reads. It did generate Cufflinks including assembled transcripts, but I can’t use these for Cuffmerge. When I visualise the folder, it points me to the correct source data. However, when I open the folder, the source data is no longer correct, but points me to different sources. I am a bit confused about these errors.
Cheers, Rik