I spent today with the scopes setup for the whole of the day, and finally got a half hour window to image.
I removed the rusted ITF from my coronado blocker earlier this year, however looking into this I found the decrease in exposure I was getting was due to an infrared leak, this was causing a blooming in the image due to thermal loading on the CCD chip - the net effect was a unpleasant decrease in the signal to noise ratio.
Things are remedied now - I have used a peice of KG3 glass in place of the ITF, this effectively blocks IR way out to 5000nm, much better than the spec of the original instrument. When conditions improve and I can actually image in blue skies this should really start to show in the Ha images... Exciting times ahead!