oooink - I have what sounds like the same problem from time to time. If so, it's your quadraceps as Peri mentioned and its typically associated with a deep (but not necessarily incorrect) kneebend, slide, and abrupt stop. It is the equivalent to stretching incorrectly. Doctors tell us to stretch and hold for x-number of seconds in a smooth, continuous stretch, not to jerk while stretching as it can cause the muscle tissue to rip. In essence, your (our) slide is smooth with a jerk on the end. It can be caused by dropping your heel, sticky approaches, or twisting the leg in your slide. I definitely have more of a problem on tacky approaches.
There are a couple of ways to help with this. Definitely stretch out your quadriceps before bowling. Warm them up. This alone should help if you're throwing a short (3-4 games) set. Make sure your foot is sliding fairly straight. If your heal is diagonal, or worse parallel, to the foul line (assuming you're not swinging a deep inside line) you'll need to learn to slide straight with that foot. Don't drop your heel (if you do) or consider the purchase of shoes with a heel that will also slide with you.
Finally, when you do get some pain, try walking it off. I've found that walking normally between shots helps lessen the pain when I'm doing the above-mentioned things incorrectly.
Good luck. Let me know if you discover anything else.
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Kill the back row