This is happening on a single workstation. User recently upgraded to new laptop.
Adobe Acrobat XI Pro
The usual signing options are not listed under 'Sign'. Only, "Sign with Certificate" is available.
Uninstall / Reinstall product
Deleted local profile data and tested under other logins, all profiles affected.
Please check for updates from the Help menu to run the latest patch of Acrobat XI i.e. 11.0.13 and check.
Is this option missing in all the PDF files or some specific one?
Could you please try running the cleaner tool "Download Adobe Reader and Acrobat Cleaner Tool - Adobe Labs" on your machine to uninstall Acrobat completely and then install the software again from here:
Check again and let me know how it appears.
Does this happen for only some PDFs but not others? If just some, then the most likely explanation is that that PDF contains [perhaps hidden] digital signatures. It can be certified or Reader-enabled (for Readers older than 11.0.7). The latter is a hidden signature. The reason that you cannot sign digitally signed PDF with a different signature type is that such action would break the existing digital signature.