This is one that costed us much time. We had some issues with textfiles that we read from a ftp server. We noticed that Powercenter uses binary transfer as default for ftp connections and we needed ascii. We read the manuals and searched the internet but couldn't find any info how to change the setting. Finally we found someone that knew how it should be done. it seems that you mannually have to add a new property in the custom properties (see screenshot):
UseFTPBinary = 0
There's a new option in the connection settings for ftp since Powercenter 8.5. You can set ASCII mode per connection instead of per integration service.