Allen said some elements of the operating system "can induce confusion", although he said he was "excited" and "impressed" by the new programme overall.
The billionaire investor has been using a preview version of Windows 8 for several months.
He said: "Windows 8 does certainly require a brief adjustment period before users become familiar and comfortable with the new bimodal operating system."
"Bimodal" is the word Allen uses to describe Windows 8's new dual operating system.
The latest version of Windows is due to be released this autumn, with the system due to undergo its biggest revolution in nearly 20 years.
Microsoft is fighting to challenge Apple and Google, which both use tablet operating systems, but it must retain the loyalty of customers who use XP, Vista and Windows 7.
In an effort to target both groups, Windows 8 will have both a tablet operating system and Windows 7, which sits alongside it.
Allen said he'd been using Windows 8 on both a desktop computer and on a tablet. But he described the dual operating system as confusing and said it was difficult to know which mode to choose when opening an application or a file.
"The bimodal user experience can introduce confusion, especially when two versions of the same application – such as Internet Explorer – can be opened and run simultaneously," he said. "Files can also be opened in either of the two available modes.
"For example, after opening a PDF attachment in Outlook from the desktop, Windows opens the file in Microsoft Reader, an application more suited for use on a tablet, rather than the desktop Acrobat Reader. A manual switch is then required to return to desktop mode."
However, Allen added that he was "impressed" with the clever idea behind the dual user experience.
"A few minor issues aside, I'm impressed with its clever integration of a bimodal interface to simultaneously support both desktop and tablet use in the same operating system.
I found the gesture navigation on the tablet to be quite satisfying and responsive. And in general, I find Windows 8 to be snappier and more responsive than Windows 7."
