The vast majority of self-directed investors say they don't understand the fees their brokers charge, and they aren't happy about it, says a new survey.

The lowest marks in the survey released today by J.D. Power and Associate went to the self-directed units at bank-connected brokerages: Wells Fargo Investments/Wells Trade, owned by Wells Fargo & Co. and Merrill Edge, owned by Bank of America Corp. .

The discount brokers not tied to full-service banks did relatively well, with broad satisfaction reported for companies like USAA, Scottrade and Charles Schwab .

Customer satisfaction on the fee question dropped significantly in the last year, even though trading commissions remained relatively low and in a narrow range of less than $10 a trade, said David Lo, director of investment services at Power. Several of the discount brokers, and not just the bank-linked ones, saw mediocre and low ratings on that issue.

The cost concerns relate to miscellaneous charges, such as inactivity and account maintenance fees, which have cropped up in brokerage accounts as they have in other financial services. Brokerage firms need to do a better job of explaining all of those fees, Lo said.

The discount brokers have been aggressive in launching high-decibel ad campaigns that tout commission price cuts, but less clear about the details of on how costs work, Powers said. Active traders often get more of the available discounts and often receive more information sources.

Only 36 percent of investors surveyed said they completely understand their commission and fee structure, down from 52 percent in 2010. Commissions are becoming less of a factor in broker choice, Lo said, because most of the commissions are not that different from each other. Most of the top-rated brokers offering trades topping out at $8.95 a trade.

USAA won the most positive ranking in its first year on the survey, and was the only firm that scored a top among the best rating.

They have excellent customer service and their reps are very well trained and very friendly, said Lo.

The rest of the top tier, termed better than most by Power, were the typically high ranked Scottrade, Schwab and Vanguard. Vanguard's scores fell, and received average marks for information resources.

Asked about Wells and Merrill Edge's weak performance, Lo said both firms scored poorly in every category, including fees, interactions, information resources and account information, account offerings and overall satisfaction.

But they are trying to figure it out, he said, adding The bank-based brokers haven't had as long to build their businesses.

We strive to do better; that's really all we can say, said Rachelle Rowe, a Wells Fargo spokesperson. She pointed out that WellsTrade, the firm's online and discount brokerage service, has only been integrated into the Wells Fargo brokerage technology platform since January. Any time you go through an integration, it's tough. We are just working to make sure our clients are satisfied with the site.

(Reporting by Linda Stern; Editing by Richard Satran)

Wells fargo Bank of america