Hi,
I thought i'd jump in here and give an operators perspective. I understand payments are important, and I know how much it frustrates you when they are late, this is in no way an excuse (In 4 years personally I've only missed payment date 2-3 times - it happens) I thought I'd let you know what happens when it comes to that time of the month for operators
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So this is what we do (it varies from company to company):
Check all of last months data for any discrepancies, errors, missing data etc - fix any problems
Run payment report and check for any errors and investigate players/affiliates if something is out of the norm
Ensure you have all correct and upto date payment details
Make sure there is enough funds in each payment method to cover commissions
Send commission for processing and wait until the payment team have sent everything.
While this sounds easy, but is something goes wrong it hold the whole process up. Not to mention any problems that happen with affiliate software, people being sick, power cuts (if your in Malta! It happened once....) Depending on the size of the program and the checks you carry out, it can be quite a time consuming process. I wish it was as easy to pressing a button or posting a cheque by mail 
Payments late for months, I can't comment on, this could be a number of reasons, it's best to ask them for an honest answer.
But like TheGooner said, most of the time it does come down to lack of man power.(when it's a few days/week late)
The best thing you can do is to have a good relationship with your AM, add them on skype etc if you can. It's often easier to get a quick answer than via email. Not that it will get you preferential treatment, but you'll get a quick answer so your not pulling your hair out waiting for a reply.
Hope this gave you a little more insight!
Head of Client Services | TAG Media