I have hyper mobility syndrome and difference in leg length, i'm always achey or hurting is this the reason why?

Possibly: Eds itself is associated with musculoskeletal pain and unequal leg lengths may be a cause of low back pain. If your pain is more generalized it is most likely related to the hypermobility.

Likely: Joint hypermobility syndrome (jhs) has a broad spectrum symptoms & degrees of joint laxity. Is common in women. Sacroiliac joint can be hypermobile &, as it shifts, invokes functional (not actual) leg length change; imparting tilting of upright body tower, widespread adaptive chronic muscle spasm, & causes fibromyalgia (my own theory). See discussions my chronic pain board at quora.Com (free).