Mine too were very short when they started budding, about 4" tall. I wrote about my concerns in a thread here. I was also worried about how dense the foliage was and how it trapped moisture. I now think that is perfectly normal for the AG Heirloom Cherry Tomatoes. It took a long time for those buds to grow into mature tomatoes and during that time the plants grew taller. They were still shorter than I expected. When the first tomatoes started turning colors (about they were probably only about 6" - 8" tall. As the first tomatoes fully ripened, the plants grew another layer above the ripe fruits and grew more buds both in the new taller part and some again in the lower part. I have picked about 70 tomatoes so far. The shortest plant is still only about 7" tall and still full of first tomatoes, and has some buds. The tallest is about 15" tall, with the first tomatoes nearly all picked but a second group growing, and buds for a third.
I did a lot of trimming, I kept the pH above 5.5. I added AG nutrients according to the schedule but also added an extra cap whenever I added a lot (quart?) of water. No water changes because I was trying to increase the PPM.
I'm getting browning leaves on top. That really bugs me. It's not a light issue anymore.
It might not be a light issue in your case, Mike. But I have burned my micro dwarf Red Window tomatoes in a Harvest with its 20 watt leds unless I keep it at least 4" over the plant. Any my Bounty with its 45 watt light has crisped them unless I keep the hood a good distance above the plants.
I also had to keep the hood high over my Sweet Heat peppers.
But, then, your peppers are doing great, so apparently that's not relative in your case. I was growing micro minis.
Maybe you could try raising the lights way above the tomatoes for 2 or 3 days and see what happens?
If it's not that, I hope you find an answer soon before the plants are too damaged.
What bugs me is how short this garden is. 7-inch tomato plants. Everything is so compact new tomatoes have to grow on top. I wonder if dimming the lights or raising the hood early on would have allowed them to grow taller. There are tomatoes coming in though.