What Causes Loose Motions When On Antibiotics For High Fever?

Hi Doctor ,
My baby was born on 28th November 2013 .
On 12th , he was crying and he had fever of 101 F . we did not know know and by the time we reached hospital his fever has increased to 102.5 F . On reaching hospital he was given Crocin and with imeediate sponging his fever subsided and he did not have fever after that . However Doctor asked us to admin him to check if he had infection . They did urine culture , blood culture etc . urine culture showed he had some UTI infection . Initially he was given ampicilling and zentalycin . After urine culture was positive he was given Amikacyn ( once per day) and zosyn( three times per day ) for one week via canula . Now he has been asked to give Clamp(amoxicillin) 1.5ml/day for next thirty days . After that doc has ashed us to DTPA for baby .
However with these antibiotics baby is passing continuous stool in small quantities somtime more than one hour continuously . While passing stool baby cries continuously :( . I feel so bad to see baby crying . Baby feeds well and when not having stool baby does very fine. We aksed doctor and they gave enterogerminal oral suspension twice per day (half ample) .
Can someone help us if he is fine and medications are ok . We feel crying after seeing all this .

REgards
A