every time i hit save or quit all the modules open up despite having saved the project with a select few.
Perhaps, you could describe your observations in greater detail. Do you mean that tool windows open, that weren't open, when you use the Save command? Do you mean that tools windows open when you try to quit the application? That would be very strange, indeed.
Also even if I change in preferences to 'open with most recent project' the dialog box still comes up and I have to choose the project i've made
We have recently discovered that the recent documents menu may not get properly updated on Snow Leopard. This is probably what you are experiencing. The problem has been corrected for the next SignalScope Pro update.