I hadn't tried with older versions, but with current release builds (3.6.0 and Forestry 1.6.2.7), the fermenter no longer recognizes saplings.

The Forestry plugin loads successfully and NEI shows the recipe.

No errors are recorded on either client or server log at launch or when placing a fir sapling in the machine, it simply does not start cooking the new sapling - but works as expected if swapped out for a vanilla sapling.

NEI's gets the recipe information from the Forestry mod...so, if Forestry reports the recipe, but Forestry's fermenter does not allow on the recipe, it is conclusively a bug in Forestry. Please report to SirSengir.