I did the same doing the stacked seed thing to save space. Thing is same color plant and type can produce three named seed titles. Orange seed / brilliant orange seed / And the way as intended by color and name. Some seeds same title as another from same plant type wont stack with each other. My plants many years old and of a few hundered seeds harvested to turn the plants deco to get dye material........ not one renewal seed.
Warpig, if you use poppy dust on a stack of the seeds that don't tell you the "type" of seed (i.e., seeds you got as a result of cross-pollination), every seed in the stack will acquire the type information. However, those seeds still won't stack with older seeds of the same type that you got from growing a parent plant of the same type (i.e., seeds from plants that were self-pollinated).
What you have to do is plant every one of the seeds from cross pollination that have been ID'd to type by using poppy dust. Then dump each seed out of its pot. If it's a brightly colored seed, it will lose the word "bright" in its label.
Once you've ID'd cross-pollination seeds, planted them, and immediately dumped them out of their pots, such seeds will successfully stack with seeds from self-pollinated parent plants. Seeds from self-pollinated parent plants that are brightly colored don't have the word "bright" in their label.
I know it sounds confusing, but if you have lots of poppy dust and lots of time and patience to plant and dump seeds, you can successfully combine those stacks of seeds a bit further.
(Poppy dust is obtained from poppy plants from peculiar seeds dropped by, among other things, wisps. Unfortunately, when you hunt the wisps for seeds, you can end up with four stacks of seeds that you can't tell apart other than that they don't stack with each other. I usually just plant 2-4 of each type and know that I'll get poppy dust and some extra plain plants to clip for dye. You get 8 poppy dust from each plant and each poppy dust has 8 charges. So if you grow each of the peculiar poppies long enough, you'll have 64 charges of poppy dust from each seed to use for ID'ing seeds. If you're short on storage space, it might be worthwhile to grow a few just to collapse a few more seeds stacks into each other.)
Edited to add:
I wonder if the Seeds of Renewal are only dropping from plants grown after a certain date.