e-trade bank is a separate entity . if you have 100k in e-trade bank and 100k with e-trade brokerage you are fine. the stock brokerage is covered separately.
Could be that you never opened a short account or that you're undercapitalized for a short account. Also, TDAmeritrade has a lot of rules and restrictions that traders can find frustrating, but these very restrictions ( insisted on by partner TD Bank ) are what keep this broker safe from bankruptcy.
once again, this proves that fancy mbas and phds are useless in the trading world. you must control your emotions namely fear n greed in the trading pit.