As I posted previously, it appears to affect both small and larger withdrawals. Though larger withdrawals, which have to draw inputs from a larger number of other transactions might have a greater probability of using some outputs which have already been used.
The comment on the article I linked to just above
(Comment #27 on http://falkvinge.net/2014/02/04/major-bitcoin-exchange-not-executing-withdrawals-now-owes-clients-38m-in-disappeared-money/ ) has a pretty good discussion of what is likely happening.
A very frustrating and annoying situation due to incompetence, but I suspect not malice.