I have this same problems with almost 100% CPU usage.

Last lines of current-Beagle file
20080106 12:05:17.8039 06414 Beagle  WARN EX: Caught exception in DoTaskReal
20080106 12:05:17.8039 06414 Beagle  WARN EX:         Tag: /home/username/.mozilla-thunderbird/fyn4mgwx.default/ImapMail/mail.somedomain.com/INBOX.sbd/varasto.msf
20080106 12:05:17.8039 06414 Beagle  WARN EX:     Creator: /home/username/.mozilla-thunderbird/fyn4mgwx.default/ImapMail/mail.somedomain.com/INBOX.sbd/varasto.msf
20080106 12:05:17.8039 06414 Beagle  WARN EX: Description: /home/username/.mozilla-thunderbird/fyn4mgwx.default/ImapMail/mail.somedomain.com/INBOX.sbd/varasto.msf
20080106 12:05:17.8039 06414 Beagle  WARN EX:    Priority: /home/username/.mozilla-thunderbird/fyn4mgwx.default/ImapMail/mail.somedomain.com/INBOX.sbd/varasto.msf ()
20080106 12:05:17.8039 06414 Beagle  WARN EX: System.UriFormatException: Invalid URI: The hostname could not be parsed.
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at System.Uri.Parse (System.String uriString) [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at System.Uri.ParseUri () [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at System.Uri..ctor (System.String uriString, Boolean dontEscape) [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at System.Uri..ctor (System.String uriString) [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at Beagle.Util.Thunderbird.NewUri (Beagle.Util.Account account, System.String mailbox, System.String id) [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at Beagle.Util.Thunderbird+Mail..ctor (Beagle.Util.Account account, System.Collections.Hashtable data, System.String workfile) [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at Beagle.Util.Thunderbird+Database+DatabaseEnumerator.get_Current () [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at Beagle.Daemon.ThunderbirdQueryable.MailIndexableGenerator.HasNextIndexable () [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at Beagle.Daemon.LuceneQueryable+AddGeneratorTask.DoTaskReal () [0x00000] 
20080106 12:05:17.8039 06414 Beagle  WARN EX:   at Beagle.Util.Scheduler+Task.DoTask () [0x00000] 

And last lines of current-IndexHelper file:

20080106 12:05:18.8091 06611 IndexH DEBUG: Generated 30 child indexables from file:///home/username/Desktop/Alice-2.0.0.tar.gz#Alice/Required/mp3/lib/ext/mp3plugin.jar (filtered with Beagle.Filters.FilterArchive)
20080106 12:05:18.8116 06611 IndexH DEBUG: +file:///home/username/Desktop/Alice-2.0.0.tar.gz#Alice/Required/tutorialWorlds/IceSkaterWorld.a2w
20080106 12:05:18.8181 06611 IndexH ERROR EX: Caught exception extracting data from archive /tmp/tmp4b3eb6dc.a2w
20080106 12:05:18.8181 06611 IndexH ERROR EX: ICSharpCode.SharpZipLib.Zip.ZipException: Data descriptor signature not found
20080106 12:05:18.8181 06611 IndexH ERROR EX:   at ICSharpCode.SharpZipLib.Zip.ZipInputStream.ReadDataDescriptor () [0x00000] 
20080106 12:05:18.8181 06611 IndexH ERROR EX:   at ICSharpCode.SharpZipLib.Zip.ZipInputStream.BodyRead (System.Byte[] b, Int32 off, Int32 len) [0x00000] 
20080106 12:05:18.8181 06611 IndexH ERROR EX:   at (wrapper delegate-invoke) System.MulticastDelegate:invoke_int_byte[]_int_int (byte[],int,int)
20080106 12:05:18.8181 06611 IndexH ERROR EX:   at ICSharpCode.SharpZipLib.Zip.ZipInputStream.Read (System.Byte[] destination, Int32 index, Int32 count) [0x00000] 
20080106 12:05:18.8181 06611 IndexH ERROR EX:   at Beagle.Filters.FilterArchive.StoreStreamInTempFile (System.IO.Stream stream, System.String extension, DateTime mtime) [0x00000] 
20080106 12:05:19.9079 06611 IndexH DEBUG: Helper Size: VmRSS=23.0 MB, size=1.81, 20.2%
20080106 12:35:19.0148 06611 IndexH DEBUG: No activity for 30.0 minutes, shutting down
20080106 12:35:19.0259 06611 IndexH  INFO: Shutdown requested
20080106 12:35:19.0320 06611 IndexH DEBUG: CancelIfBlocking Beagle.Daemon.ConnectionHandler
20080106 12:35:19.0350 06611 IndexH DEBUG: (1) Waiting for 2 workers...
20080106 12:35:19.0353 06611 IndexH DEBUG: waiting for server '/home/username/.beagle/socket-helper'
20080106 12:35:19.0356 06611 IndexH DEBUG: waiting for HandleConnection (5)
20080106 12:35:19.0495 06611 IndexH DEBUG: Server '/home/username/.beagle/socket-helper' shut down
20080106 12:35:19.0507 06611 IndexH DEBUG: (2) Waiting for 1 worker...
20080106 12:35:19.0511 06611 IndexH DEBUG: waiting for HandleConnection (5)

I'll exclude /tmp from indexing, let's see what happens.