Were the users you can't see ever subscribers? They may still be marked as such and Unity wont show you them for import until they're cleaned of those properties (which can be done with the Remove Subscriber Properties tool you'll find in Tools Depot).
If not, are these users in a particular container/OU? Anything about these users that ties them together? Unity isn't going to arbitrarily not show them, and I don't have much info to go on here... I suspect they were marked as subscribers since this is by far the most common cause of such a problem.
