OK, its early days, but I think after 2 days of testing that I might have got to the bottom of my GPU workunits taking 40-50 mins.
I went down the whole reducing clock speeds route, which did diddly squat..
Watching the task manager, all 4 cpu's were maxed out 100%, and the clue came from watching the load time for the cpu to pass a wu to the gpu, on some wu's, it was taking 2 mins before I saw any sign of crunching. This coupled with some earlier comments over gpu usage levels (mine were all over the place!) made me think that the cpu was possibly the cause
Playing around with the <avg_ncpu> value, it would seem that the long workunit times was down to a cpu bottleneck, one cpu couldn't keep the gpu's fed fast enough.
After playing around with multiple wu/card combo's I have set the following
<avg_ncpu>0.223333</avg_ncpu>
This means I have 2 cpu's crunching and 2 feeding the gpu's
I lose an additional processor, but in 12 hrs I have not had a wu take longer than 28:49

at stock clocks
Task manager is showing average cpu usage of around 92-95%, that is with 2 cpu cores crunching and 2 feeding the gpu's which are running 3 wu's each
My gpu usage is also steady at around 92%
This means that I have slightly more playing around with the <avg_ncpu> value as there is a 5% headroom, which is wasted at the moment.
I will of course be ramping the clocks on the gpu right back up to the 800's as soon as I can..
Thank god for that - it was really bugging me!
Toxic - you can give loudbob a slightly gentler slap now as Im in a good mood again