Had a look and think I know what the problem is, namely the //emphasis// matching that's going on.
The entry pattern for emphasis is;
'entry'=>'//(?=.*//)',
See the class
Doku_Parser_Mode_formatting here -
http://dev.splitbrain.org/view/darcs/dokuwiki/inc/parser/parser.php - the '$formatting' property is where this is defined.
It uses a "lookahead" regex expression to check that there's a closing // before entering the state. Unfortunately that matches 'http://'
Meanwhile auto-URLs are allowed inside emphasis so when it actually finds the string 'http://www.bar.com' this gets eaten up as an "auto-URL" token leaving the Lexer in the emphasis state, searching for it's closing // token (which has now been consumed by the URL)
The following example demonstrates this;
=== START example ===
Anything below **this** line is not rendered.
* Some text//foo More text
http://www.bar.com
This line and the list item are not rendered.
// < close the emphasis
But this line is now rendered normally and everything after it
=== STOP example ===
Note this problem would effect non-auto URL's as well e.g.
* Some text//foo More text [[http://www.bar.com]]
Not entirely sure what the best fix would be - perhaps a special character class in the lookahead expression which explicitly ignores the string '://' but that's definately a hack.
Another simple option might be to ban links for //this syntax// and require <em>this instead</em> if URL's are needed.
Thinking about anything more than that makes me think the solution would be painful.
Technically this could be a problem with some of the other formatting syntax e.g. __underline__ and **bold**, where there to be any other Dokuwiki syntax that might conflict with them.