When I use a aux battery it used to buff emergency power to shields, but now it does nothing at all as a buff to EPS. Really hinders me in gameplay, makes me dead hehe.

An AUX Battery has never buffed Emergency Power to Shields. An Aux Battery rasies auxiliary systems power and will report Aux system if they are down. Auxiliary Systems power doesn't affect Shields, either. A Warp Core Engineer DOFF and Science Team will boost EPtS.

A combined Auxiliary/Shield Battery will increase both. You probably got some from a duty officer mission or lock box.