Was Jesus unsure if the temptation in the desert was God talking?

No, but the temptation was rejected specifically on the grounds that it did not agree with scripture. Therefore, the same grounds can surely be used in other, similar situations, including those where one is unsure of who is talking.

For those unaware of how the story goes:

• Jesus goes into the desert, and fasts for 40 days. After this, He is somewhat hungry.
• The devil turns up, and asks Him to turn some stones into bread, for food (thus, symbolically, treating the physical needs of the body as the most important thing).
• He refuses, citing old testament scripture: "Man shall not live on bread alone, but on every word that comes from the mouth of God."
• The devil tries again, quoting scripture and basically telling him 'if you throw yourself from this cliff, you will be safe, for God will protect you. If you are the Son of God, why not prove it?'
• Jesus refuses, again quoting scripture; "Do not put the Lord your God to the test"
• For a third temptation, the devil shows him all the kingdoms of the world, and offers to give tham all to him - "if you will bow down and worship me". A direct appeal to greed.
• Jesus again quotes scripture, "Worship the Lord your God, and serve him only.", and the devil leaves, unsatisfied.