(Read more: Marc Faber: Apple "could go bust")
Greenlight also remains convinced that Green Mountain Coffee Roasters is overvalued, in part because of allegedly misleading sales figures.
"It is impossible to reconcile GMCR's piecemeal disclosures with its financial statements, and the new CEO repudiates straight math," the letter said, noting that Greenlight had added to its short position in the company.
The letter pointed out what it said were "holes" in the bullish case on the coffee company. They include questions about brewing machine sales figures, manufacturing capacity for coffeemaker pods (called K-Cups) and demand for a brewing machine set to be released in late 2014.
The stock fell more than 5 percent in heavy late afternoon and after-hours trading, presumably in response to the letter.
Spokespeople for Green Mountain did not immediately respond to a request for comment.
(Read more: Einhorn closed winning short bet on JCPenney in Q2)
Greenlight also said it had initiated a "medium-sized" long position in Osram Licht, a German lighting company.
"OSR is unlevered, has financial flexibility, and given that the financial targets were set in the context of a spin-off, we suspect OSR may ultimately exceed targets," the letter said.
The fund's largest long positions at the end of September were Apple, General Motors, gold, Marvell Technology, Oil States International and Vodafone, according to the letter.
Greenlight also said it had exited two profitable long positions: Norwegian insurer Gjensidige Forsikring (a 27 percent return) and Oaktree Capital Group (a 28 percent gain).
Greenlight managed $9.7 billion in hedge fund assets as of July 1, according to the Absolute Return Billion Dollar Club.
A spokesman for Greenlight declined to comment.