Third line is...

3/28/2010 9:18:51 AM log flags: file_xfer, sched_ops, cpu_sched, sched_op_debug

O.K, that at least shows cc_config.xml is in the correct location & working,
you can now turn off those Extra flags, and <use_all_gpus> by changing the 1 to a 0,
Note the task log should have been set to on, as it's on by default,
Now check in the Activity Menu that it's selected to Run based on preferences and not to Always,

Edit: you do get two lines in Boinc's messages saying the following?:

28/03/2010 18:09:40 Config: don't compute while RelicCOH.exe is running
28/03/2010 18:09:40 Config: don't compute while DAOrigins.exe is running

Claggy

OK, so it is working now (had it set to run always, not based on preferences). I feel dumb for not trying that in the first place.

3/28/2010 7:14:53 PM SETI@home Restarting task 08mr07ae.12359.72.3.10.85_1 using setiathome_enhanced version 603
3/28/2010 7:14:53 PM SETI@home Restarting task 08mr07ae.12359.72.3.10.71_0 using setiathome_enhanced version 603
3/28/2010 7:14:53 PM climateprediction.net Restarting task hadsm3dhet2_kd9a_006626832_2 using hadsm3 version 607
3/28/2010 7:14:53 PM SETI@home Restarting task 08mr07ae.12359.72.3.10.70_1 using setiathome_enhanced version 603
3/28/2010 7:15:07 PM Re-reading cc_config.xml
3/28/2010 7:15:07 PM Re-read config file
3/28/2010 7:15:07 PM log flags: file_xfer, sched_ops, task
3/28/2010 7:15:15 PM Suspending computation - an exclusive app is running
3/28/2010 7:15:45 PM Resuming computation
3/28/2010 7:15:49 PM Milkyway@home Sending scheduler request: To fetch work.

It doesn't list the exceptions, but it is at least following them. Thanks for your help and patience.