Do you mean it did not activate at all?
Or when you try to preview/publish markdown formatted content?
What is your WordPress version?
I just did not look if it works after seeing the message. WP 3.8.1 on a test blog – no other plugin and default theme.
Tested using the same configurations (WP 3.8.1, no other plugin, default theme), everything is fine!
Where does the message appear? I might have missed it!
Fixed!
Problem:
Installing Jetpack Markdown using ‘Widgets -> Add New -> Upload’, and trying to activate it right from the “Plugin installed successfully” page causes a missing/invalid header error.
Installing Jetpack Markdown using any method does not cause any errors.
Activating Jetpack Markdown from the Plugins admin page does not cause any errors.
Cause:
WordPress is reading the headers of jetpack-markdown/markdown/easy-markdown.php instead of (or before) jetpack-markdown/markdown.php.
Solution:
Make the header section in easy-markdown.php invalid to WordPress.
Notes:
New downloads will have this issue fixed. I didn’t increment the version number to keep the convention (same version number as the original Jetpack).
Thanks you everyone (and Gunnar Hellekson)