I am a bit bewildered at your description. If you have additional water trapped in your hoses, it would amount to having lesser wort than you started with. From this, I gather that you are able to collect that wort.
Which means that somewhere along the way, your process losses (mash tun dead space, boil of rate, loss to trub, grain absorption) are not what you have them set for in your profile or your measurement of starting water is off. Before you set the mash tun dead space for a negative 1.25 gal, what did you have it set at? How are you measuring in your starting water? Can you export your last brew with your measured values as a .bsmx file and post it?