So the situation is resolved and I would like to tell those who are interested how it was resolved.
We are now getting S/N ratios exceeding the spec for reserpine for the 609 to 195 transition.
The error occurred as a result of putting the probe together incorrectly, not that the parts were put in wrong. If you are familiar with the Waters Quattro Premier XE. When the ESI Probe was re-assembled, a piece of PEEK tubing was used on one side of the PEEK union (which was used to bottom-out the ESI Capillary, I imagine the capillary could have gone through the centre hole as well). However, the PTFE "Tube Liner" was not bottomed-out on the tube stop of the PEEK Union, this created a dead volume.
When re-assembling the probe ensure that the PTFE Tube Liner is bottomed-out in the PEEK Union. In our lab we have noticed that these liners are not cut squarely, it was suggested that we trim off as little as possible from the PTFE Tube Liner to ensure that it is squarely cut before installing it, this will reduce the dead volume.
Thank you all very much for your responses. If anyone else expriences this problem, I hope I have been able to help!
Cheers,
Tom