Fst Differences Between Mature Trees and Seeds
I will assume the claim Clearly there is genetic differentiation between population 1 and 2 in seeds, but not much in adult trees. is correct and that you have done your stats correctly.

A complete analysis of the situation depends of how you calculated Fst. Did you use Weir-Cockerham Fst or standard Nei's formulation? How did you average (with or without weights) over population and loci? But without going to these details, here is an extreme scenario that explain why you could observe such patterns.

Imagine, the migration rate from any population and to any population is 0.5. In such case, in absence of selection you would not expect any divergence between populations. However, if genotypes AA and AB both have seed survival probability of 0 in pop2 (but not in pop1), then pop2 will be fixed for A2A2 at the adult stage even though when looking at the seeds you cannot see any evidence of divergence.