Volume Problem when using external midi instruments

Hi everyone, I'm having a problem recording the audio from my external midi instruments into Logic 8.
I have all my external midi instruments set up in my environment and they are all going through a motu micro lite interface, with the audio going through a focusrite saffire pro 40.
The way I record Midi into Logic is to load up a new software instrument-select external instrument-find the relevant synth & input-record the midi that I want & adjust as needed-bounce down to an audio channel.
The problem Im having at the moment and have had for a little while is that when I record this way, the audio that accompanies the midi, although I can hear it loudly through my monitors, the input levels in Logic are really small and when I come to bouncing down and listen back to it, it is a lot quieter than I'd originally heard.
With the Pro 40 comes the Mix Control surface, upon checking this the volume on the master output channels is much more representative of the volume I'm hearing through my monitors, and it isn't the same within Logic. I've checked that I haven't got an output coming through channels on this at the same time as its coming through Logic which would result in the sound being doubled and obviously louder, this definitely doesn't appear to be the case.
Its really puzzling and quite annoying me, If anyone could shed any light on why this may be happening that would be fantastic, I've used this forum a few times and I've always found people to be very kind & helpful.

I've checked that I haven't got an output coming through channels on this at the same time as its coming through Logic which would result in the sound being doubled and obviously louder, this definitely doesn't appear to be the case.
It was the first thing I was thinking about. Stop the "Software Monitoring" in the Logic Prefs and try again if you do not have any duplicated hardware routings.
!http://img59.imageshack.us/img59/4967/aglogo45.gif! [www.audiogrocery.com|http://www.audiogrocery.com]

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