In particular, pricing for its hosted Business Productivity Online Suite (BPOS) -- which includes hosted versions of Exchange, SharePoint, LiveMeeting and Office Communications -- is causing customers some concern, said Paul DeGroot, an analyst with research firm Directions on Microsoft.

If a customer purchases a BPOS subscription for employees who will access only those services, the customer must still purchase CALs for those users, DeGroot said, even though they are not accessing the on-premise software as well. Microsoft gives customers a discount on other parts of their license in such scenarios -- on the Software Assurance (SA) maintenance program required for enterprise agreements, for example -- but they still end up paying for something they are not using, DeGroot said.

Depending on how it wants to give companies access to Azure beyond the pay-as-you-go pricing model, the company could run into the same trouble with its cloud-computing platform, he said. "With Azure it could get even more complicated," DeGroot said, though it remains to be seen until Microsoft unveils specific terms of Azure's integration into enterprise contracts.

To mitigate any complexities, Hauger said Microsoft is, on request, giving customers options for how they can license Azure, pricing that is separate from software they already pay for.