This is a known issue with the 192 version of Botania that the (somewhat derpy) FTB modpack team decided to put in just about every pack with Botania yet chooses not to update with the fixed any other version (191 it doesn't occur and 193 is fixed. We're at 197 in the version cycle for Botania...). Flowers will automatically link when placed, so if you are able to automatically break and place the flower every now and again, your automated set ups will be fine (break using sticky piton on the block beneath and place with golems/rannuncarpus?).
Yes well at least I'm pretty sure I haven't had to rebind them since then and they all still make mana.
Hey SirWill, thank you so much for fixing these, had been troubling us all for a while. Can I ask how it was done (just for reference in how the fix was made)?
botania is open source. you could just look at the fixed versions and see what he did different and bytecode edit this into the server files. -> fixed botania Not sure if he did it that way.