Why is the word Muhammad pronounced differently in kalimah and tashahhud?

The subject ism inna is always in the accusative case mansūb (منصوب), and the predicate khabar inna is always in the nominative case marfū (مرفوع) 

(http://corpus.quran.com/documentation/ particleinna.jsp).

What this means is that if the word anna is not used, then the word Muhammad will have the ‘u’ sound at the end. If the word anna is used, then the word Muhammad will have the ‘a’ sound at the end. In the kalimah, we say: Muhammadur Rasulullaah. In the tashahhud (in adhan and iqamah), we say: Ash-hadu anna Muhammadar Rasulullaah.