Ya, I had a similar problem with my Clam Mac Client.  For me, it saw the Clams on restart, however as I was on support chat with Clam tech, he said "Rescan".  But alas, I found a hefty amount of Clam and I need not rescan.  It's worth it. 

I actually mined 5 coins since that time.  Having missed out on the mining phase of crypto so last year, finding an extra coin in my client in the morning is quite rewarding!