Alien Biomes does have a changelog entry for 0.6.2 that seems to be related to your finding.
Some trees have additional tile restrictions. This prevents grassland trees from appearing on dirt and dryland trees appearing in desert.
But I can't seem to reproduce this. Could you elaborate a bit?
I downloaded the latest version of Factorio (1.1.27), got Alien Biomes 0.6.4 and the current version of this mod (1.1.1) and it seemed to work fine. I tried in 2 new games across different biomes and it worked as intented. New trees are created from existing nearby trees without issues.