We had the same issue with a Windows application accessing xls files in code. We run it with Citrix on Windows 2008 64 bit and for us, the suggestion to compile at least the executeable project with the "Platform target" property set to "x86" instead of "Any CPU" was the solution (the only one as we have no access to the Citrix server farm).
See here:
http://ybbest.wordpress.com/2009/07/22/the-microsoft-ace-oledb-12-0-provider-is-not-registered-on-the-local-machine/.
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