Definitely. Though you could fix that problem relatively easily.
I think you might even be able to run von Neumann's method first, but store the coin flips; and then once you've got enough stored, extract a few more bits from the already used flips.
Perhaps like this:
When you do two flips, you add one of three possible tokens to your list:
'double-heads', 'double-tails' or 'mixed'.
Crucially, you only store 'mixed' and not whether it was 'head-tails' or 'tails-heads' because that information was already used to produce the von-Neuman-bit.
After your list has 1000 entries, you run an algorithm a bit like what I originally described to extract bits. The complication is that the table you construct has all possibilities of shuffling a fixed number of 'double-heads', 'double-tails' or 'mixed' tokens.