Just to be clear - it is completely impossible for shaking the vials to have a direct effect on peak shape. BUT, it is possible for shaking to affect something that affects peak shape. In this case, as Rod says, you probably have a slight overload / defocussing effect due to more ethanol getting to the column.

Increasing the split ratio is quicker and easier than changing a loop, so try that.

10 min is too short an equilibrium time, even with shaking, and will adversely affect repeatability. Be aware that when you increase it the peaks will get bigger (this is the main symptom of incomplete equilibrium) and the overload effect will get worse.

What column are you using (phase and dimensions), what is the gas flow rate, and what is the temperature programme ?

Peter