Todays Big Stock: Microsoft (NASDAQ: MSFT)

Like a rude party guest, Microsoft’s (Nasdaq: MSFT ) timing always seems to be off. Less than a month after spending $8.5 billion on Skype, Microsoft saw the VoIP carrier’s software choke on an errant file, keeping some users from logging in and making calls yesterday.

“A small number of you may have had problems signing in to Skype. This predominantly affects people using Skype for Windows. We have identified the problem and will issue a fix in the next few hours,” the company wrote in a blog post. (Emphasis mine.)

All seems to be well now — for the record, I never had a problem — but the company’s steady parade of headlines like these must infuriate investors such as Greenlight Capital’s David Einhorn. He’s calling for Steve Ballmer to resign, saying Mr. Softy’s longtime CEO has spent shareholders’ cash on “ill-conceived mergers and acquisitions,” as The New York Times DealBook blog reports it.

Einhorn also says Ballmer is out of touch with the major market trends that have lifted the fortunes of Apple (Nasdaq: AAPL ) and Google (Nasdaq: GOOG ) in recent years. I disagree. He’s not out of touch — he’s off-key. Ballmer has no sense of timing.

Look at the Skype deal. Two years ago, eBay (Nasdaq: EBAY ) sold what amounted to a two-thirds stake in the VoIP leader for $1.9 billion. Now Ballmer has agreed to pay well more than twice that. Timing is everything, in life and in acquisitions.

To be fair, there are technical reasons for Ballmer to make the deal. Bundling Skype into Microsoft’s Office suite makes sense, and adding video calling to the Dynamics CRM product could disrupt salesforce.com (NYSE: CRM ) . Yet there’s also sure to be a ton of integration work needed, all of which must be done in a way that satisfies 700 million Skype accounts and 170 million active users.

Is that tradeoff really worth the company’s $8.5 billion price tag? Where’s the upside? Microsoft can’t simply be after Skype’s 700 million accounts. Mr. Softy is the world’s leading supplier of computer software. Its customer base numbers in the billions.

The only logical reason to buy the VoIP leader, then, is for its features. Frankly, I have doubts that Skype’s network is that much better than the varying alternatives, especially when small-business VoIP specialist 8×8 (Nasdaq: EGHT ) is growing outrageously. Why spend $8.5 billion when 8×8 commands just $210 million in market value as of this writing?

We’ve been over this before, I know. I’m raising these questions again because Einhorn did, too, when he alluded to “ill-conceived mergers and acquisitions” in his remarks. He’s clearly concerned about Ballmer’s ability to squeeze value from the Skype deal.

Yesterday’s technical hiccup won’t mean much to the overall equation. But it’s still a blemish for a company that’s suffered far too many for far too long, at far too high a price for shareholders. In that sense, I can appreciate Einhorn’s frustration.