This is not anything that I have encountered myself but like you mentioned there could be something for orders that are meeting a particular criteria. It can be very difficult to track down sporadic issues, if there is a problem with the weight or something like that you should be able to get it down to a set of steps that can reproduce the issue. This will be the key to determining what the problem could be.
If you expect it to be a weight related issue try adding an extremely high value for the weight in the cart, you could set the quantity to a high value for a heavy item.
If the issue is just a random occurrence you will not be able to make it repeat with any regularity. You mentioned that this has only happened a couple of times, how many orders have you processed in relation to the bad shipping value orders?
