I can not reproduce this:

code:
1 <?php
2 $dummy = null;
3 echo "Breakpoint set";
4 echo "End";
5 ?>
command log:
Connect

<?xml version="1.0" encoding="iso-8859-1"?>

<init xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" fileuri="file:///home/httpd/html/test/xdebug/bug284.php" language="PHP" protocol_version="1.0" appid="23578" idekey="dr"><engine version="2.0.0RC5-dev"><![CDATA[Xdebug]]></engine><author><![CDATA[Derick Rethans]]></author><url><![CDATA[http://xdebug.org]]></url><copyright><![CDATA[Copyright (c) 2002-2007 by Derick Rethans]]></copyright></init>

(cmd) breakpoint_set -i 6 -t line -f file:///home/httpd/html/test/xdebug/bug284.php -n 2

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="breakpoint_set" transaction_id="6" id="235780001"></response>

(cmd) run -i 7

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="run" transaction_id="7" status="break" reason="ok"><xdebug:message filename="file:///home/httpd/html/test/xdebug/bug284.php" lineno="2"></xdebug:message></response>

(cmd) stack_get -i 8

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="stack_get" transaction_id="8"><stack where="{main}" level="0" type="file" filename="file:///home/httpd/html/test/xdebug/bug284.php" lineno="2"></stack></response>

(cmd) step_over -i 11

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="step_over" transaction_id="11" status="break" reason="ok"><xdebug:message filename="file:///home/httpd/html/test/xdebug/bug284.php" lineno="3"></xdebug:message></response>

(cmd) stack_get -i 12

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="stack_get" transaction_id="12"><stack where="{main}" level="0" type="file" filename="file:///home/httpd/html/test/xdebug/bug284.php" lineno="3"></stack></response>

(cmd) step_over -i 14

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="step_over" transaction_id="14" status="break" reason="ok"><xdebug:message filename="file:///home/httpd/html/test/xdebug/bug284.php" lineno="4"></xdebug:message></response>

As you can see it correctly goes to line 4. Do you perhaps have other commands that your log is missing - and do my line numbers match with yours?

Sorry missing a breakpoint at line 3.

Command log:

breakpoint_set -i 4 -t line -f file:///var/www/coop/stepover.php -n 3

breakpoint_set -i 5 -t line -f file:///var/www/coop/stepover.php -n 2

run -i 12

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="run" transaction_id="12" status="break" reason="ok"><xdebug:message filename="file:///var/www/coop/stepover.php" lineno="2"></xdebug:message></response>

step_over -i 16

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="step_over" transaction_id="16" status="break" reason="ok"><xdebug:message filename="file:///var/www/coop/stepover.php" lineno="3"></xdebug:message></response>

step_over -i 19

<?xml version="1.0" encoding="iso-8859-1"?>
<response xmlns="urn:debugger_protocol_v1" xmlns:xdebug="http://xdebug.org/dbgp/xdebug" command="step_over" transaction_id="19" status="break" reason="ok"><xdebug:message filename="file:///var/www/coop/stepover.php" lineno="3"></xdebug:message></response>

Fixed in CVS, thanks for your report.