>In Greek the feminine ending commonly is *-a: (long), and the neutral
ending is *-a (short). >I can easily explain it inside Miguel's hypothesis
as *-a: < *-eyh2, and *-a < *-eh2. But if >the both are derived from the
same original *-eh2, how can we explain this difference?
There is no difference originally.
Neither the Greek nor the Latin short -a in the neuter plurals is original
in thematic stems. Latin shows good evidence of long -a: in earlier texts
(and even one example in Virgil!) By the Classical period, it had been
shortened. In Greek, consonant stems had the ending -&2 (syllabic -h2),
while vowel stems had the ending -VH2, which > long -a: in thematic
stems, -ia, -ua etc elsewhere. So the feminine ending and the neuter in
thematic stems were identical.
Peter