I have experienced the same problem since I started a few months ago. I transferred 0.01 coins from my mobile wallet to Armory but it never fully synced with the network. The application would crash somewhere during a database scan and I never saw my coins again.
I did check on bitref.com and saw that the coins were still there, it was just a matter of Armory not seeing the transactions.

Now I tried again, with the latest testing (windows) client, and did Rescan Balance -- this fixed the problem for me!