Hello,
Some one correct me if i'm wrong but i believe this is by design.
The FSEQ file is the rendered output of the xml file and as such should only contain the data necessary to turn on and off the channels in the different universes. It would not contain the timing tracks and effects that you can edit.
The XML files show up correctly because they contain the following pre-rendered data; sequence timing, song data, color palettes, timing tracks, and effects. This does allow it to be edited in xlights and then rendered to an FSEQ file.