It should show the correct value from the beginning. I don't think anything is going to change once you have sent a transaction. As you can see on my screenshot, I also opened a 0.002 BTC channel and I was able to send about 90% of the funds.

I suspect that this might be because of the node you are connected to. It sounds as if the required channel reserve was extraordinarily large. Would you mind sharing the id of your peer either here or via a private message? No one will be able to find your channel because Electrum creates private channels which are not advertised across the network.