After a fresh checkout the executable bit is correctly recorded on files:<pre>
$ ls -l unix/configure
-rwxr-xr-x 1 rkeene users 581812 2011-02-26 22:37 unix/configure*
$ fossil artifact | grep unix/configure
F unix/configure x
$
</pre>

However, after updating to a tag that lacks the file, and then updating to a tag that includes it the executable bit is missing:
<pre>
$ fossil update core-8-0-2
...
updated-to:   1998-04-29 17:09:47 UTC
$ ls -l unix/configure
ls: cannot access unix/configure: No such file or directory
$ fossil update core-8-5-9
...
updated-to:   2010-09-08 17:38:32 UTC
$ ls -l unix/configure
-rw-r--r-- 1 rkeene users 569172 2011-02-27 13:34 unix/configure
$ fossil artifact
B
...
$ fossil artifact | grep unix/configure
F unix/configure x
</pre>