PS Paycycle psnt vs unix

During my life time of implementing PS, it has always been a standard to configure the Paycycle to the psnt.  We have a situation, we did our development on the psnt and have just been informed we can only use unix.  When we run all the processes the formats of all files and document are totally messed up.  All files are coming across as one line.  The checks are not the same format and are missing the micr.  We are using BI Publisher and are on 9.2.  Is this a layer of security or is there some configuration that needs