Second this. Perhaps it was the fact that the balance shows as zero when you have orders in the system ? For instance, on MtGox, if you put in a sell order for 10 BTC, then the balance will still show 10 BTC, untill that order is matched, on Btc-e.com the last time I traded it was not like this, so if you had 10 LTC in your account, and then put them as a sell-order, then your LTC balance would show as 0, untill the sell order was matched, whereafter your USD or BTC balance would increase to accomodate for the sold LTC. However, simply cancelling the LTC sell order, will show your real balance.
A smarter way of solving this would be to perhaps show funds as available and in active orders.
Not any active orders:
LTC available: 10
LTC active sell orders: 0
LTC total balance: 10
One active order:
LTC available: 5
LTC active sell orders: 5
LTC total balance: 10
Or something similar. Currently it's shown as:
LTC : 0
when you have a sell order for all of your LTC, however, if you click on the relevant menuitem, you'll find your active orders, and by cancelling those - the LTC balance will go back to what it was. So the LTC are not lost.