<div class="slides">
<section data-markdown>
<script type="text/template">
|h1|h2|
|--|--|
|a|b|
</script>
</section>
</div>

<div class="slides">
<section data-markdown="content.md"
data-separator="---"
data-separator-vertical="--"
data-separator-notes="^Note:"
data-charset="iso-8859-15">
</section>
</div>

Sorry, this may be a non-issue. Tables with external markdown is now working for me and I'm not sure what I changed.
I'm seeing the same problem. Tables in external markdown don't work for me.
Found the problem. I had the data-separator="---". This caused problems with the table header row. Changing it to data-separator="^---$" did the trick for me.
Most helpful comment
Found the problem. I had the
data-separator="---". This caused problems with the table header row. Changing it todata-separator="^---$"did the trick for me.