I having some weird issues with the patch as well on umbraco 4.0.2.1. 

I've seen a few other posts here regarding some issues/questions, but my current issue doesn't seemt o fall in line with those :(

First off, it would not apply using the package and told me to apply manually.  It appears that the package could not change the web.confg or 404handlers.config files only drop the dll and aspx pages.  Anyway to fix this manually I did the following:

• Verified the dll was here /bin/Umbraco.PoetPatcher.dll
• Verified the error page aspx here:  /umbraco/plugins/PoetPatcher/CustomError.aspx
• Modify /config/404handlers.config to look like this:

<?xml version="1.0" encoding="utf-8" ?>
<NotFoundHandlers>
    <notFound assembly="umbraco" type="SearchForAlias" />
    <notFound assembly="umbraco" type="SearchForTemplate"/>
    <notFound assembly="umbraco" type="SearchForProfile"/>
    <notFound assembly="umbraco.PoetPatcher" type="GenericError"/>
</NotFoundHandlers>

• Modify the web.config to look like this (change the customerrors tag to this):

  <customErrors mode="On" redirectMode="ResponseRewrite"
defaultRedirect="~/umbraco/plugins/poetpatcher/CustomError.aspx" />

•  Removed the custom error id from the 'errors' tag in the /config/UmbracoSettings.config file:

  <errors>
      <!-- the id of the page that should be shown if the page is not found -->
      <!--        <errorPage culture="default">1</errorPage>-->
      <!--        <errorPage culture="en-US">200</errorPage>-->
      <!--<error404>1115</error404>-->
    </errors>

The above seems correct to me, but I get the following behavior.  I've restarted the service and app several times to no avail:

• When I vist this URL "/test" - I get my old 404 page (even though I removed it from web.config customErrors *and* removed the entry from the "errors" tag in UmbracoSettings as shown above.
• Visit "/umbraco/plugins/test" - I get the old 404 page (same as above)
• Visit "/umbraco/plugins/test.aspx" - I get the the proper CustomError.aspx page
• Visit "/test.aspx" I get the old 404 page

Now, I do use the SEO URLs (enabled via web.config using the following):

 <add key="umbracoUseDirectoryUrls" value="true" />

Anyway, I'm at a loss right now, hopefully someone has a clue to what could be happening.  I'll keep trying to figure this out in the meantime :(