Boil-off is the most likely factor.
Partial mash could also be a factor. One thing it took me time to figure out when going to partials from extract plus specialty grain is that extract has a lot volume. If I took 5.5 gallons of water, added 6lbs of LME, and boiled for an hour, I ended up with a post boil volume of just over 5 gallons. When I went to partial mashing, I was initially doing the same thing and landing just under 5 gallons because I was losing half the volume of the LME I was adding in a full extract batch. I had to add that volume back in as mash water to get my post-boil volume right.