I am trying to use org-mode to write nice tables that I can use with pandoc and latex, so I end up converting pipe table in markdown to grid tables in markdown.

However, it seems that a blank link in a pipe table confuses markdown when converting to a grid table. Using pandoc 1.15.2.1, I start with the following MWE as test.md:

| test  | header |
|-------+--------|
| first | row    |
|       |        |
| third | row    |

and run pandoc test.md -t markdown-pipe_tables-simple_tables-multiline_tables to obtain:

+--------------------------------------+--------------------------------------+
| test                                 | header                               |
+======================================+======================================+
| first                                | row                                  |
+--------------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------------+
| third                                | row                                  |
+--------------------------------------+--------------------------------------+

where there are missing pipes for the second row.

Sorry, I should have commented here too. #2616 is a different issue. I caught it while looking at this issue and wondering why one would use a markdown reader to read org-mode tables. The answer to this seems to be that the org mode reader makes things even worse.

I haven't spent much time on this, but it seems like the above hints at a bug in the markdown writer.

Thanks @tarleb! Also, the reason I want to use org-mode tables is that the table editor works so much better for me than table-mode in Emacs. So many problems putting in links and the like when editing with table-mode. Ugh.