Sounds like your custom program is opening the com port and keeping it open or busy while the IFI loader is trying to open the port. Your programmers should be able to fix this by having their custom program close the port before the IFI loader attempts to use it. As most programs will not try to use the serial port if it is already in use by another program.
Also you may want to be more descriptive in your posts, by telling us that you have a custom com-1 output this could mean hardware or software, and what it does we don't know you are more likely to get responses and help if the person reading your post doesn't have to guess at what you meant or what is going on. Also com-1 is the designation that windows uses for the first logical serial port. Also spell check is a feature that you should always use before you submit your post. Welcome to the CD community and we love to help others and share information, just try to be a bit more descriptive about things in your posts
