If you don't wish to pay for OEM batteries, something which I'm personally on the fence about despite the only spare batteries I've purchased so far being Canon branded, then I would suggest looking through the forums for the widely supported third party batteries. From memory I would go after brands like Wasabi, SterlingTek, and a third brand that is slipping my mind seem to be the most commonly mentioned in a positive light and widely praised. They aren't the cheapest, but still cheaper than Canon by a good margin, and are companies with a reputation of producing a solid product and helping their customers, and I would trust their quality control and manufacturing standards far more than a battery that's only selling point is being dirt cheap.
Picking up a new canon branded battery from a reliable dealer may also be a good idea simply for a reference point. (Or borrowing one from another photographer) Trying to sort out what is going on when there are lots of different variables at play is not a great and fun thing.
Personally I don't see a huge impact on long IS use on my Sigma 150-500, and that lens has a rather long focus throw as well, and I would be exceptionally surprised to hear that the lens you were using drained that so much juice from a normal battery as to impact shot count to such a degree.
Canon EOS 7D | EF 28 f/1.8 | EF 85 f/1.8 | EF 70-200 f/4L | EF-S 17-55 | Sigma 150-500