Wow that is pretty odd. I would suggest taking a look at
TradeKing if you want low commissions and decent execution. Their trades are $4.95 with options running $.65 per contract.
You can view our speed
Tradeking Review here on the site as well.
How long have you been using Etrade for and how long has the timeouts been going on for? I wonder if there is some setting that effects this or what because obviously that is really a problem.