I have a solid explanation of what may be causing your problem but must admit that what follows includes one very big assumption. And that assumption is that your mashes typically drop in temperature over time. Even if you are using an all-in-one system where wort is heated either in the lower section of the mash tun/brew kettle or externally before it is returned to the mash, mash temperature often drops because these systems are not well-insulated.
Over the last three years I have brewed what I consider to be great beers using an all-in-one system. During this time of exploration, I have noticed things that are very different to what I became accustomed to during my 26 years of commercial brewing using mash mixers in a wide range of sizes. When a steam-heated mash mixer is used, mash temperature is uniform with a slow drop in temperature during rests. And when the temperature eventually drops below about 1 °F (1⁄2 °C) from the set point, mash is automatically stirred and heated back to the set-point. As cooking processes go, these temperature changes are slow to occur and tightly controlled.
My guesstimate about what is happening with your brews is that you mash-in at some temperature between 149–158 °F (65–70 °C) and hold for about 60 minutes before commencing wort recirculation. During your mash rest, you don’t stir and may or may not heat. And even if you do heat using an all-in-one brewing system, your system is measuring the wort temperature in the bottom of the mash/kettle and controlling the temperature to the set point. I want to put that on hold because you may not be using this sort of system.
Let’s assume you are mashing in a non-heated vessel like an insulated cooler and performing a protein rest versus a single-temperature mash. With the protein rest, you mash in at about 122 °F (50 °C) and rest for about 30 minutes. Now it’s time to heat, and you add heat while stirring. The heat may come from hot water, hot mash if you are decocting, or external heat from a flame or electric element. Whatever you are doing, you are probably stirring your mash to keep the temperature uniform. And you are also exposing the starch being solubilized during the protein rest to beta and amylase enzymes.
The same basic process is different when you skip the protein rest because you probably do not stir your mash during your mash rest. Simply stirring the mash increases extract dissolution. And stirring the mash during heating steps helps to maintain temperature uniformity; something that all-in-one systems don’t do very well. Without jumping down a very deep rabbit hole, I have a few suggestions.
For starters, if you have an all-in-one system, measure the mash temperature and compare it to your set point. If there is a big difference, which I have seen in my own experience, determine the offset and increase your target temperature to provide enough heat from wort to make up for the mash heat losses to the environment. It’s critical for yield for alpha amylase to be active in the mash where it reduces mash viscosity and increases starch solubility.
If you are not experiencing much heat loss during mashing, extend your mash time to account for the time reduction when you dropped the protein rest. While you’re at it, give your mash periodic stirs to help move starch from your malt into wort. My gut tells me these details are the root of your issues. But because I work for a malting company, I would be remiss not to suggest checking your mill gap/malt crush, mash thickness (thinner mashes improve yield), and thermometer calibrations as part of this troubleshooting exercise. Hopefully this answer points you in the right direction in searching for those lost extract points!