MSS(E) generates the following error on startup:

Event Type: Error
Event Source: Office Server Search
Event Category: Gatherer
Event ID: 10036
Date: 2/12/2009
Time: 4:30:12 PM
User: N/A
Computer: SEARCH

Description:
A database error occurred.
Source: Microsoft OLE DB Provider for SQL Server
Code: 2812 occurred 1 time(s)
Description: Could not find stored procedure 'dbo.Profile_GetAliasList'.

This is a known issue and can be safely ignored, according to Microsoft:

https://connect.microsoft.com/feedback/ViewFeedback.aspx?FeedbackID=309900&SiteID;=480

Microsoft Search Server suffers from the same issue as SharePoint Search of not being able to crawl SSL-forced sites, however, it is able to crawl non-Default Zones.

In order to allow MSS(E) to crawl an SSL enabled site, extend the site to a new Zone in the SharePoint Central Administration.  You may enable SSL on the extended site, but you cannot force SSL on the site (which is done via IIS).

Once you’ve done this, configure the SSP for MSS(E).  On the Search Server, go to Crawl Rules.  Create a new Rule and use the following options as they appear in the image:

Note that it is important to use an asterisk after the site URL (/*), otherwise Search Server will only crawl the root of the URL.  It is also important that “Do not allow Basic Authentication” is unchecked.

Next, if this extended site is not the Default Zone, go to Search Server Mappings and create a new mapping.  Enter the URL of the extended site under “Address in Index”, and enter the original site URL in the “Address in search results”.  This will transform the crawled URL into search results the users are able to access.

The next time MSS(E) crawls the site, you should be able to get results from your searches.  You can also check the Crawl Log on the Search Server Administration site and verify there are no errors.

You may encounter this error in the Application Event Log after installing MSS(E) in your farm:

Event Type:        Error
Event Source:    Office SharePoint Server
Event Category:                Office Server Shared Services
Event ID:              6482
Date:                     5/4/2009
Time:                     11:00:49 AM
User:                     N/A
Computer:          SEARCHSERVER

Description:
Application Server Administration job failed for service instance Microsoft.Office.Server.Search.Administration.SearchServiceInstance (b2ef3361-3f34-41e4-8e2a-56cbd5fc78f4).
Reason: Access to the path 'C:\WINDOWS\system32\drivers\etc\HOSTS' is denied.

Technical Support Details:
System.UnauthorizedAccessException: Access to the path 'C:\WINDOWS\system32\drivers\etc\HOSTS' is denied.

For what ever reason, Microsoft wanted Search Server to edit the HOSTS file on the MSS(E) server.  In order to resolve this error, provide the WPG_ADMIN group with Modify NTFS permissions to the %windir%\System32\drivers\etc directory.  If you restart the Search Server service, the error should not appear after making that modification.