new equipment profile seems to be causing problems

Would love anyone's feedback that might have some insight to my issue. I've been using Beersmith for a couple of years now with no problems. I've always hit my target gravities within a point or two, and usually on the high side. I've been trying to improve my accuracy, and not try to squeeze every last drop of wort out of my kettle so I recently modified my equipment profile to reflect trub/ chiller and fermenter losses which I had not previously accounted for. I've brewed three batches with this new profile and on all three of them have missed my target gravity by 10-12 points, on the low side. What's interesting is that when I scale a recipe to the new profile, my 'Est. Mash Eff' on the design tab of Beersmith jumps way up, from about 73-74% before to 84, 85, 86% now, depending on the recipe. It doesn't seem like this estimated efficiency should do anything to my actual recipe but it does seem odd that I'm missing by 10-12 points and that estimated percentage has jumped up by 10-12 percent. Is this just coincidental? Anyways, I'm quite frustrated to be missing my gravities all of a sudden when I've been consistently hitting targets for the past couple of years. If anyone has any insight into what I might be doing wrong with this profile I'd really appreciate your thoughts.

Here are the numbers I had for my profile before:

Brewhouse efficiency: 72%
Hop utilization: 100%

Mash tun vol: 13 gal
Mash tun weight: 13 lbs
Mash tun specific heat: .3 (cooler)
Lauter Tun deadspace: 0

Top up water: 0
calc. boil vol: checked
boil time: 90 min
boil off: 1.5 gph
use as hourly rate: checked

Loss to trub and chiller: 0
Top up water: 0
Batch volume: 5 gal
fermenter loss: .25 gal

With the new profile the only changes I made were changing the trub/ chiller loss to 1 gal. and the fermenter loss to .75 gal. and these changes caused my estimated efficiencies shift dramatically. Does anyone know if that estimated efficiency actually affects my recipe? I would think not, since it's only an estimate and I have not changed the number for my brewhouse efficiency.

One workaround that I tried was to just change my batch size, including those trub/ chiller and fermenter losses into the batch size and when I did that my estimated efficiency stayed where it was before, at 74%. I haven't brewed with the profile using this workaround and I'm not sure if or how it will affect my other numbers, but I'd prefer to be able to plug the numbers into the right place in the profile and not need to deal with any workarounds.

Thanks for any feedback

BeerSmith uses your brewhouse or overall efficiency as a constant.  When you add more wort losses, like you did, BeerSmith adjusts your mash efficiency to make up the difference in sugar concentration.  [backwards from my perspective, but this is how it is]. 

So, when you add more losses to your water balance, you need to adjust your brewhouse efficiency to accommodate this added loss.  Start with your efficiency was 72% with your old system with 5 gallons collected and (just a stab here) 1.3 gallons lost to grain absorption, plus 1.5 gallons lost in boil for a total water usage of 15.8 gallons.  If you add 0.5 gallons of water to remain in your kettle after filling the fermentor, your new water volume would be 16.3 gallons.

To reflect this in your efficiency, take your standard 72% efficiency times the former volume and divide that by the new volume to get an initial estimation of what that efficiency would be.  Thus:

72% * 15.8 gallons / 16.3 gallons gives you an overall efficiency of around 69.8%. 

This should result in the same mash efficiency of your first profile.  Use the next brew to dial this in a bit more accurately by measuring the volumes and specific gravity throughout the system to get an accurate water and sugar balance.  Plug the numbers into BeerSmith and adjust the profile to match.

Thanks Oginme. This makes sense. I'll adjust according to your feedback and hopefully be back on track for my next brewing session.