Venkat pinged me today and said that they were unable to view log or output files of concurrent requests in a fresh clone. When you clicked on View Log or View Output button the new page which opened showed Internal server error.
The Apache error_log showed errors like this one:
Premature end of script headers: $COMMON_TOP/html/bin/FNDWRR.exe
Metalink Note 390989.1 talks about applying patch 3288588 and relinking FNDWRR.exe. However we are already on ATG RUP6 which includes this patch. So we just relinked FNDWRR.exe on the web node. However the error persisted.
Akhilesh ran autoconfig on a hunch. The issue was resolved after autoconfig. We still don't know what was causing the issue, but the straight solution is to run autoconfig.