There is a difference between the settlement period (3 days) when buying/selling stocks in a cash account, and the actual settlement of deposited funds.ACH transfer, where it pulls it directly from your bank has a holding period of 5 or 10 days for non-marginable securities. I think your initial account deposit is 5 days, and additional deposits thereafter are 10 days.
Best thing I've found is to always wire your funds. They get deposited within a few hours, and there is no waiting period to use those funds as with an ACH transfer.