Wasn't able to reproduce this problem using version 5.1, 6.1, 6.4 or the upcoming version 7. What version are you using? Can you post the exact syntax you're using for the fancytable plugin?
When I used Plugin Edit to amend a FancyTable, submitting a change causes all line breaks in the table body to be removed.
The PluginEdit shows a field "Rows separated by in the header; for the table body, one row per line. Cells separated by | in both cases."
After creating a working FancyTable with table body rows like this:
row 1 cell 1 | row 1 cell 2
row 2 cell 2 | row 2 cell 2
after submitting/inserting the plugin edit tool this changes to:
row 1 cell 1 | row 1 cell 2 row 2 cell 2 | row 2 cell 2
Is this a bug? Can I change an admin preference? Is there a workaround, I tried inserting Wiki end of line code to no avail.