Well first of all, is the vet you brought your gecko to a reptile specialist vet? Or is it just a multi-pet practice vet who will treat reptiles? If this vet is not well versed in all things reptile then often they do more harm then good by giving poor information or misdiagnosing. Why is your gecko on baytril? Is there an infection? Did your vet do a fecal sample?
You need to provide a thorough history of your gecko and its husbandry in order to help us to give you advice. However i must stress that this sounds as if the situation is getting worse and your best bet might be to find a really good reptile vet asap.
How long have you had your gecko? Where did you get him from?
How old is it?
Is it housed alone or with others?
Was it eating well prior to the vomiting and diarrhea?
What are the temps? How are you measuring them?
How is the cage set up - what substrate was used initially? How many hides? How is it heated?
If a fecal sample wasn't run, you should do that immediately as parasites may be a problem.
If the temps are low (lower than 88-92deggresF in the warm side measured by digital thermomter) then you need to increase them as this can lead to poor digestion - vomiting and diarrhea.
Have you been soaking your gecko at all? Often times antibiotics will dehydrate reptiles which makes them feel even worse - a nice swallow (not over the sholders) warm water (95-100degreesF) bath once a day will help to maintain hydration.
Without knowing more information its hard to guess what might be going on. Again, i must stress that if the vet who saw your lizard was not a reptile specific vet or is not very well versed in reptiles then i would try to find a reptile specific vet to look at your leo as well.
please give us the above information and good luck with everything!
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0.1 Bearded dragon (Hannabil)
0.1 mexican Black kingsnake (Morticia)
2.1 Leopard Gecko's (Pogo,Jeffrey Nothing, Louise)
0.0.1 Tokay Gecko
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1.0 Blood Red Corn (Virus)
0.0.1 Mali Uromastyx (Scuttle)
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4.1 Cats (Poe, Tucker, Abhid, Felicity, Emmy)