That's a quirk of Windows batch files. It passes control to the 
application processed in the command. Unless that process continues your 
processing, the whole thing stops. However, if you precede the command 
with "call", the batch file resumes after the called process stops. Thus, 
the output you want is:

call fop -fo app_AdmSpm.fo -pdf app_AdmSpm.pdf
call fop -fo app_AQis.fo -pdf app_AQis.pdf
call fop -fo app_AusbildungVorOrt.fo -pdf app_AusbildungVorOrt.pdf
call fop -fo app_Bestad.fo -pdf app_Bestad.pdf
call fop -fo app_Bipa.fo -pdf app_Bipa.pdf
call fop -fo app_Bmz.fo -pdf app_Bmz.pdf
call fop -fo app_Elz.fo -pdf app_Elz.pdf
call fop -fo app_Elze_Bz.fo -pdf app_Elze_Bz.pdf

Jay Bryant
Bryant Communication Services