Up to vXI we used "Windows Integration" in Security:Advanced to tell Acrobat to look to the CAPI store for cert chains. That seems to have disappeared in XI and my SmartCard signature cert is being declared "invalid" by Acrobat and I'm not being allowed to sign. Thoughts?
Instead of the "Security" category, Acrobat XI moved that option to the "Signatures" category. Select the "More..." button from the Verification area and you should get a "Signature Verification Preferences" pop-up. At the very bottom of it you'll find the expected Windows Integration options.