Baytril injection site reactions are discussed in this thread: http://www.ball-pythons.net/forums/s...d.php?t=105021 Reactions that I have looked at microscopically involved muscle damage, so the assumption that they can be prevented by injected into muscle is false. In fact, the current recommendation is to inject Baytril subcutaneously (under the skin) and to dilute the dose with saline. I don't think anyone has examined whether or not external factors (live UV exposure) contribute to this phenomenon, interesting to think about.
I would follow the vet's instructions and get your baby to the herp vet on Friday if possible. S/he may change antibiotics or adjust the dosing regime.
Typically Baytril is given every 48 hrs, based on scientific studies that have examined how long therapeutic levels are maintained in the blood in some species of reptiles. However, we don't know if the vet you saw last night is giving a lower dose or has another reason for giving more frequently.
Bottom line is, follow vet instructions as close as possible, don't sweat a couple hours more or less than every 24, and get to the qualified herp vet as soon as you can.