Still can't seem to duplicate on 6.1. Tried using the help and plugin edit as you mention and also switched back and forth between wysiwyg and wiki mode.
Perhaps there's a setting messing things up. Does changing the "wiki paragraph formatting" settings at Admin Home > Editing and Plugins help? Or some of the Wysiwyg settings at Admin Home > Wysiwyg? Shouldn't make a difference but I'm running out of ideas! Sorry I'm not more help - perhaps someone else can replicate.
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.