I use Blesta for my web hosting company. I have used WHMCS for a few years, before that I used ModernBill (they were purchased and died off), and I've used ClientExec. They all have pros and cons.
What I like about Blesta is that it's clean and the developers are actively involved in the community. If you compare the customer base, I'm sure WHMCS wins in numbers, but I promise you they don't win on support, helpful community, or code security.
Problems? Not really. I'm a little crazy with wanting things to work a certain way, so I'm always digging into things to make them work. But, not issues at all really with Blesta.