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The outlook for retailers reporting September same-store sales on Thursday offers substantial improvement over September 2012, but there are significant downside risks to the early estimates. Research firm Retail Metrics estimates that same-store sales will rise 4.1% year-over-year in September compared with a rise of just 0.8% last year.

Better-than-expected automobile sales in September provide some encouragement for the retailers, but the back-to-school shopping season was overall a disappointment. Teen retailers Abercrombie & Fitch Inc. (NYSE: ANF), American Eagle Outfitters Inc. (NYSE: AEO), and Aeropostale Inc. (NYSE: ARO) are expected to post numbers worse than the double-digit sales declines they put up in the third quarter.

Retail Metrics also notes that big ticket items like appliances, home furnishings, and cars took some of the steam out of sales of soft goods.

Among the chain stores expected to post good gains are Walgreen Co. (NYSE: WAG), which had a terrible September last year same store sales down 11.1% making the comparison much easier this year. Same-store sales at Walgreen are expected to rise 6.5%.

Another winner is PriceSmart Inc. (NASDAQ: PSMT) where Retail Metrics estimates sales will rise 8% on top of a same-store sales rise of 10% in September 2012.

Consumer confidence in the U.S. economy had declined even before the federal government shutdown, and that could weigh on September sales. Worse, depending on how long the shutdown lasts and how much brinksmanship we’ll see over raising the federal debt ceiling, retailers could go into the all-important holiday shopping season facing some serious headwinds.