Superficial muscle overwork, whilst deep cores ones do nothing +Hypermobility

Since my stay in hospital my muscles have deconditioned. Research by Keer & Simmonds suggests that muscle tissues atrophy greatly in the first 5-7 days during inactivity, particularly the endurance slow-twitch muscle fibres (Keer, 2003, Simmonds, 2003). Additionally, and interestingly, muscles also atrophy in response to pain and fear (Simmonds, 2003).I am not doing very well. Although I had paced my activity up again and managed to walk around my park (normally I now manage to jog around 3/4 of it). My superficial muscles are still grossly overworking at the expense of the deep core ones which are just doing nothing. This is an extremely frustrating situation and one that for reasons I do not fully understand seems to happen regularly to hypermobile people. At some point, the deep core muscles do reactivate but until they decide to activate I have to play a waiting game. The reason for this switch in the wrong muscles -e.g. superficial muscles massively overworking at the expense of the deep core ones is not something I understand. It is very irritating and means I go back to hanging into all my joints until the deep core ones decide they will bother to activate. I know that 9 days in hospital in bed hasn't helped much and although I am trying my best - including trying pelvic tilts and other things to encourage their awakening, I am pretty much stuffed until the deep core ones ignite. Do any physios or other medical experts reading this have any thoughts or theories?