serial port configuration problem

I'm not sure if this is an Acer question, hardware, software, or Windows, but if anyone can explain the particular idiocy I have run up against it would be much appreciated anyway. I have an old Acernote Light I'm trying to install some equally old educational software on for a children's technical course. The problem is the serial port (only one on the laptop) which is used to control a remote interface. When the technical software is started, it says the port isn't working (it sees it, though). If I then restart the computer in DOS mode, then immediately type 'Exit' to restart in Windows, everything works fine until the next reboot, when it all has to be done over again. Obviously this must have something to do with initialisation of the port, but the procedure described here is the only way I have found so far to get around this. I would really appreciate some help if someone can tell me how to set whatever needs setting permanently, or at least automate the process via autoexec.bat. The laptop is an AcerNote Light 370pc, originally running Win95 with a 98SE upgrade installed over that.