Wow that’s terrible. We’ve used paypal for over a decade and have never had any issues with the virtual payment system. That said, we used to have a lot of clients pay in this manner as they wanted to use credit cards, however we’ve shifted over 90% of our payments to direct deposit, avoiding fees. 3% adds up to a lot of coin over a year. The only drawback is that we have to rely upon clients to pay as opposed to having control with the card on file to charge. Fortunately our clientele has changed to larger business who don’t play around with late pay or no pay, they simply automate the deposits. Ultimately, the 3% charge from paypal was well worth the risk of clients paying late or trying to stiff us.
If you use quickbooks, they also have a payment system that is integrated into your invoicing making the whole model seamless. I believe it’s pretty much the same fee – about 3% for most credit card transactions, but they are big and a bit more reputable when it comes to processing and their customer service is spot on.