Flipboard users counting on the social magazine to retain their Google Reader subscriptions after the service’s shutdown last night are waking up today to a bit of disappointment. Though Flipboard had promised earlier that those who signed into Google Reader in their Flipboard would be able to continue to enjoy their subscriptions after Reader’s closing, apparently, that’s not the case.

On Twitter, many are tweeting their confusion and unhappiness with the situation, and, as one TechCrunch reader has pointed out, users can no longer take to Flipboard’s GetSatisfaction page to discuss the issue further, as Flipboard’s community page was also shutdown a couple of weeks back. There, the company had only posted a few responses to users’ technical questions and suggestions related to the Reader shutdown, and mainly directed people to company blog posts for more information.

When Google first announced its plans to close Google Reader back in March, Flipboard, like many other services in the news reading business, quickly announced its plans to serve as a new home for abandoned Google Reader users.

“Your Google Reader subscriptions will be safe on Flipboard,” the company’s blog post began before outlining a few key steps for users to take to make sure their feeds remained intact. The set up described was simple – users only needed to establish a Flipboard account, connect their Google Reader account in the settings, and then remain signed in. Flipboard said there was no need for any other actions on the user’s part, and that “your feeds will be saved.”

In June, Flipboard again posted a reminder about the Google Reader shutdown, repeating those same steps.

But a good number of tweets as well as private tips to TechCrunch this morning, indicate that something has gone wrong. Instead of seeing a collection of news feeds in Flipboard, users are merely presented with a message that reads “no content.”

Given that Flipboard had already been serving as a Google Reader client of sorts ahead of the transition, it makes sense that the company would want to continue to serve that audience. It’s unclear at this time what has happened, and whether it’s a temporary bug or a more serious technical miscalculation on Flipboard’s part.

We’ve reached out to Flipboard to find out what the issue is, and the company is now looking into it. We’ll update when we hear back.

According to at least one tipster, his set of folders and feeds was restored as of just a few minutes ago, but it only included feeds that were already in Flipboard’s system. Many of those he had archived in Google Reader were not recognized.

More to come.