I know this has been reported somewhere else but thought it might be worth highlighting.
Just attached a brand new machine and got the following stack of 'unrecoverable error's and 'file not found's:
15/09/2006 08:54:41||Fetching configuration file from http://docking.utep.edu/get_project_config.php
15/09/2006 08:55:07|http://docking.utep.edu/|Scheduler list download succeeded
15/09/2006 08:55:07|http://docking.utep.edu/|Sending scheduler request to http://docking.utep.edu/docking_cgi/cgi
15/09/2006 08:55:07|http://docking.utep.edu/|Reason: Requested by user
15/09/2006 08:55:07|http://docking.utep.edu/|Requesting 259200 seconds of new work
15/09/2006 08:55:09|http://docking.utep.edu/|Scheduler request succeeded
15/09/2006 08:55:09|Docking@Home|New host venue: work
15/09/2006 08:55:09|Docking@Home|Successfully attached to Docking@Home
15/09/2006 08:55:11|Docking@Home|Started download of file charmm_5.2_windows_intelx86
15/09/2006 08:55:11|Docking@Home|Started download of file 1tng_mod0001_309_464230.inp
15/09/2006 08:55:15||Rescheduling CPU: project suspended by user
15/09/2006 08:55:22|Docking@Home|Finished download of file 1tng_mod0001_309_464230.inp
15/09/2006 08:55:22|Docking@Home|Throughput 111889 bytes/sec
15/09/2006 08:55:22|Docking@Home|Started download of file grid_probes.rtf
15/09/2006 08:55:23|Docking@Home|Incomplete read of less than 5KB for grid_probes.rtf - truncating
15/09/2006 08:55:23|Docking@Home|Temporarily failed download of grid_probes.rtf: HTTP file not found
15/09/2006 08:55:23|Docking@Home|Giving up on download of grid_probes.rtf: file was not found on server
15/09/2006 08:55:23|Docking@Home|Started download of file lpdb_amino.rtf
15/09/2006 08:55:23|Docking@Home|Checksum or signature error for grid_probes.rtf
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_309_464230_2 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Deferring scheduler requests for 1 minutes and 0 seconds
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_5_360861_1 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_310_146050_0 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_6_203280_1 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_266_460274_1 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Deferring scheduler requests for 2 minutes and 8 seconds
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_10_83476_1 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Deferring scheduler requests for 4 minutes and 1 seconds
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_11_196595_1 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Deferring scheduler requests for 16 minutes and 30 seconds
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_253_75405_1 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Deferring scheduler requests for 26 minutes and 21 seconds
15/09/2006 08:55:24|Docking@Home|Unrecoverable error for result 1tng_mod0001_13_205618_1 (WU download error: couldn't get input files:<file_xfer_error> <file_name>grid_probes.rtf</file_name> <error_code>-163</error_code> <error_message>file was not found on server</error_message></file_xfer_error>)
15/09/2006 08:55:24|Docking@Home|Incomplete read of less than 5KB for lpdb_amino.rtf - truncating
15/09/2006 08:55:24|Docking@Home|Temporarily failed download of lpdb_amino.rtf: HTTP file not found
15/09/2006 08:55:24|Docking@Home|Giving up on download of lpdb_amino.rtf: file was not found on server
15/09/2006 08:55:24|Docking@Home|Started download of file lpdb.prm
15/09/2006 08:55:24|Docking@Home|Checksum or signature error for lpdb_amino.rtf
15/09/2006 08:55:25|Docking@Home|Incomplete read of less than 5KB for lpdb.prm - truncating
15/09/2006 08:55:25|Docking@Home|Temporarily failed download of lpdb.prm: HTTP file not found
15/09/2006 08:55:25|Docking@Home|Giving up on download of lpdb.prm: file was not found on server
15/09/2006 08:55:25|Docking@Home|Started download of file lpdb_probes.prm
15/09/2006 08:55:25|Docking@Home|Checksum or signature error for lpdb.prm
15/09/2006 08:55:26|Docking@Home|Incomplete read of less than 5KB for lpdb_probes.prm - truncating
15/09/2006 08:55:26|Docking@Home|Temporarily failed download of lpdb_probes.prm: HTTP file not found
15/09/2006 08:55:26|Docking@Home|Giving up on download of lpdb_probes.prm: file was not found on server
15/09/2006 08:55:26|Docking@Home|Started download of file 1tng_mod0001_5_360861.inp
15/09/2006 08:55:26|Docking@Home|Checksum or signature error for lpdb_probes.prm
15/09/2006 08:55:37|Docking@Home|Finished download of file 1tng_mod0001_5_360861.inp
I see this post is some days old. Are you still having the same problem, or is 'issue closed'?
Sorry, went on holiday so no reply before today. :S Haven't actually checked if this is till happening (only got back this morning) but will try it again later today and see what happens.