do a video gait analysis in bare feet, i guarantee you all problems will have disappeared. it's the shoes that screw you up.
from another thread:
Wearers of expensive running shoes that were promoted as correcting pronation or providing more cushioning experienced a greater prevalence of these running-related injuries than wearers of less expensive shoes (Robbins and Gouw, 1991). In another study, expensive athletic shoes accounted for more than twice as many injuries as cheaper shoes, a fact that prompted Robbins and Waked (1997) to suggest that deceptive advertising of athletic footwear (e.g., "cushioning impact") may represent a public health hazard. Anthony (1987) reported that running shoes should be considered protective devices (from dangerous or painful objects) rather than corrective devices, as their capacity for shock absorption and control of over-pronation is limited. The modern running shoe and footwear generally reduce sensory feedback, apparently without diminishing injury-inducing impact–a process Robbins and Gouw (1991) described as the "perceptual illusion" of athletic footwear. A resulting false sense of security may contribute to the risk of injury (Robbins and Gouw, 1991). Yessis (2000, p.122) reasoned that once the natural foot
structures are weakened by long-term footwear use, people have to rely on the external support of the footwear, but the support does not match that provided by a well functioning foot.
Measurements of the vertical component of ground-reaction force during running provide no support for the notion that running shoes reduce shock. Robbins and Gouw (1990) reported that running shoes did not reduce shock during running at 14 km/h on a treadmill. Bergmann et al. (1995) found that the forces acting on the hip joint were lower for barefoot jogging than for jogging in various kinds of shoe. Clarke et al. (1983) observed no substantial change in impact force when they increased the amount of heel cushioning by 50% in the shoes of well-trained runners. Robbins and Gouw (1990) argued that plantar sensation induces a plantar surface protective response whereby runners alter their behavior to reduce shock. The less-cushioned shoe permitted increases in plantar discomfort to be sensed and moderated, a phenomenon that they termed "shock setting". Footwear with greater cushioning apparently provokes a sharp reduction in shock-moderating behaviour, thus increasing impact force (Robbins and Hanna, 1987; Robbins et al., 1989; Robbins and Gouw, 1990). However, in these studies the subjects ran on treadmills or force platforms. Further studies are needed to establish how shoes affect impact force and shock-moderating behavior on natural surfaces such as road or grass.
Other features of footwear, such as arch supports and orthotics, may interfere with shock-moderating behavior and probably hinder the shock-absorbing downward deflection of the medial arch on landing (Robbins and Hanna, 1987). These features reportedly reduce pronation and supination or offer the wearer lateral and arch support. They may help some people with foot pathologies, but their benefit is uncertain for runners with healthy feet (Yessis, 2000, p.121).
http://sportsci.org/jour/0103/mw.htm