This is probably not strictly a nautilus bug.  But is damn annoying.
What is happening is a mismatch in the mime-type definitions.  In my
case, (and I am using fedora 6, though I suspect Ubuntu will have the
same issue and fix - s/o please test) the freedesktop.org.xml file in
/usr/share/mime/packages lists the .exe extension as being
"x-executable", when it should rather be "x-ms-dos-executable" and the
Description field lists executable, instead of "DOS/Windows executable".
Here is what it looks like (with out the language stuff):

<code>

  <mime-type type="application/x-executable">
    <comment>executable</comment>
    <magic priority="40">
      <match value="\177ELF" type="string" offset="0">
        <match value="1" type="byte" offset="5">
          <match value="2" type="little16" offset="16"/>
        </match>
      </match>
      <match value="\177ELF" type="string" offset="0">
        <match value="2" type="byte" offset="5">
          <match value="2" type="big16" offset="16"/>
        </match>
      </match>
      <match value="MZ" type="string" offset="0"/>
      <match value="0x521c" type="little16" offset="0"/>
      <match value="0420" type="host16" offset="0"/>
      <match value="0421" type="host16" offset="0"/>
      <match value="0603" type="little16" offset="0"/>
    </magic>
    <glob pattern="*.exe"/>
  </mime-type>

</code>

The fix (workaround) that works for me is to edit
/usr/share/mime/packages/freedesktop.org.xml (as root) and change the
following lines:

<code>

  <mime-type type="application/x-executable">
    <comment>executable</comment>

</code>

change to

<code>
  <mime-type type="application/x-ms-dos-executable">
    <comment>DOS/Windows executable</comment>
</code>


Once this has been done, you need to run (as root): "update-mime-database 
/usr/share/mime"

This should correct the problem.  Other filename extensions can get
mixed up, but the fix should basically be the same.  Check the
/usr/share/mime/packages directory for references to the wonkified
extension or mime type and then edit the offending file to correct it.
Once done, run the update-mime-database command to apply the changes to
the system and bob's your uncle.

Cheers
Sneezy da Leprechaun

-- 
nautilus's clever anti-hax0r detection is really dumb
https://bugs.launchpad.net/bugs/19101
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