Portal flash does not mean success
The battery is just barely enough for the portal jump, as far as I see. A lot of time all the white segments get completed and the portal flash occurs, but then you stay in the source system. Console says that there was insufficient energy, and lists an error from portal's L2L about trying to execute a local which is nil.
I am not sure whether it is a related problem, but even if the jump succeeds, there is a good chance to be on an orbit quite far from the target portal (and incompatible with appearing close to a portal with wrong speed).