
Grasshopper, if you're working with only a handful of programs it's easy to keep track of where you're owed money and who owes you what.
While I think the OP may have been foolish for letting their account run down like that, personally I have sites actively sending traffic to 150+ affiliate programs (adult and mainstream) and keeping track of accounts can be a complete fucking nightmare. It requires the services of a trusted book keeper several times a month. The traffic can't be consolidated because many of the programs offer unique products.
That's just me and a few outsourcers, and you'll find that with operations that are much larger and more professional than mine that sometimes missing payments and missed thresholds won't be noticed for months, whilst traffic in particular niches comes and goes with the fluctuations of the serps. This is kind of like that situation and Clickbank is taking advantage of that in a way that literally no other affiliate program does.
It doesn't actually cost CB anything to hold your money - in fact, you're giving your cash to them interest free in the same way that you do with a Paypal balance. While it may be listed as a liability on their balance sheet, it's still cash they have to use (and eventually pilfer from you) in the mean time.
So, while CB might have a few good products for odd niches, in other ways they suck balls. Much like how Paypal fills a need, but it basically sucks balls as well.