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I don't know about difference in chargeback rates, etc, but I can tell you this... We use our own merchant account, and Netbilling handles our transactions. We did this because we had 2 3rd party billers go out of business on us in a row, without paying us. The downside is that you have to be even more careful about chargebacks. They'll terminate your merchant account in a second. Definitely less worries with a 3rd party biller, but then you're putting a lot of faith in them.
That probably didn't help a bit. Sorry.
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