This isn't possible. At least, not the way you first attempted it. The vanilla block system has a hard limit that keeps all geometry between -16 and +32 on every axis. Once you go beyond those limits, in your case above 32y, the game throws an error and your model fails.
The way to do this is to give the top and bottom halves of a double-tall flower separate models. Make the bottom half the normal 0y-16y, but have the top half extend to 32y. Because the top half already has a 16y offset due to it being one block above the base it'll appear that the entire thing extends three blocks high even though in reality it's only two blocks high, and only a single block to place. It seems like you did this, but have the UVs backwards on one of the two blocks. They need to match.
So to fix this I tried adding "randomOffsetX: false", "randomOffsetY: false", "randomOffsetZ: false" to the JSON files. I found the idea for this fix here.
But nothing happened, and the offset remained.
Can anyone think of a fix, or an alternate way to achieve a 3 block high cornstalk? This is really puzzling me.
To cover what Alvoria didn't:
1. Random offsets are no longer controlled by models anymore (if you didn't notice, that thread is 2 years old and the model format was not in a stable version yet, it was still being worked on), it has gone back to hardcoded. Just look at any of the models of stuff that DOES have random offsets, you will see there is nothing within the model to cause it.
2. It looks to me like the bottom half of your sunflower isn't textured properly. Notice how it doesn't meet in the middle like it should, this isn't a random offset because the offset would make the model move (not the texture). Either you used the wrong UVs or you did the rotation on the bottom half incorrectly (not setting "rescale":true like the default cross model does, or maybe you didn't set the origin to 8,8,8?)
EDIT: Also fun to read back on that thread, both me and Alvoria are in it. Alvoria doomsaying and I posting on the good things of the format (including the random offset that you found, haha). Though I was completely wrong in thinking models would help my pack (it seems models didn't really influence the popularity of packs besides the model-only packs that sprung up, many already popular packs add a few models)
Also, I'm starting to feel even more bitter now seeing that many of the problems with resource packs we have now are the same ones we've had 2 years ago. Not too long ago I repeated an almost word-for-word comment on sounds not being able to be looped...
Rollback Post to RevisionRollBack
"I'm an outsider by choice, but not truly.
It’s the unpleasantness of the system that keeps me out.
I’d rather be in, in a good system. That’s where my discontent comes from:
being forced to choose to stay outside.
My advice: Just keep movin’ straight ahead.
Every now and then you find yourself in a different place."
thanks guys! I managed to get it to work. it was the UVs. Using Cubik to make planes and rotate them into a cross formation wasn't working, so I ended up copy/pasting the code from the block/cross.json file and changed the names of the textures, and the coordinates for the UVs, and the top and bottom matched up perfectly. thanks!