I've read through all of this and I was having the same issues. I had recently switched away from using a cooler to a direct fire setup. I just utilized the "stainless kegs" in beersmith for my setup b/c it is very similiar. I made four or five batches on it and nothing was turning out good. I was measuring my efficiency and it was low. I had been treating my water, I crush my own grains, had been hitting good ph, etc and I couldn't necessarily dial it in. So on this last one, I paid a great deal of attention to my boil off, trub loss, chill loss, etc. I took pre boil measurements and found that I was hitting in the mid 90's with my mash efficiency; however, I was losing a lot more to trub, cooling, etc. Also, I wanted to start shooting for 10 gallons bottled, which affected my "batch size." I took what I learned from this last brew and backed into everything on beersmith and compared it to what I actually got. If I would have had the correct numbers in for equipment and batch size, I would have hit an efficiency in the 80's. Essentially, because I have now reconfigured my equipment profile and what I am targeting, I had to readjust my recipes by adding a little more grain to increase OG. Once I really started playing with the software, I found it quite interesting and it was a good learning experience. It taught me a lot about my process. Hopefully, this will solve the problem of things tasting "watered down" and a lack of malt profile from beers that I know were spot on with temp, ph, etc.
This was just my experience and I thought I would share it with you. Maybe it will help, maybe it won't.....good luck!