Please show the code you use to log.

Running as an Apache 2.2.11 module.  (Windows XP SP3)

Error handling and logging section from php.ini
===============================================
error_reporting  =  E_ALL
display_errors = Off
display_startup_errors = Off
log_errors = On
log_errors_max_len = 1024
ignore_repeated_errors = Off
ignore_repeated_source = Off
report_memleaks = On
track_errors = Off
error_log = "/path-to-logs/php/error.log"


Simple web page that blows up
=============================
<?php 
	ini_set('max_execution_time', 1);

	$i = 0;
	do {
		echo "$i\n";
		sleep(1);
	} while ($i++ < 10);
?>


Log file after accessing the above page twice
=============================================


[21-Dec-2008 19:02:07] PHP Fatal error:  Maximum execution time of 1 second exceeded in \path-to-test-page\46916.php on line 10

[21-Dec-2008 19:03:11] PHP Fatal error:  Maximum execution time of 1 second exceeded in \path-to-test-page\46916.php on line 10


Note the extra <CR>s.

PHP only adds PHP_EOL (in your case \r\n) to the log messages so that extra \r comes somewhere else.

This was actually an escaping problem by caused by using the same log for both 5.2.7 and 5.2.8.  Checking previous error logs, I notices at ALL lines are terminated with \r\r\n.  Do to some unusual escape sequences in the file the log file view I was using became confused about the termination character.  Starting a fresh log file rectified the problem.