Software install/uninstall in dual-boot

My PC has dual-boot installed (Win98SE & Win2000 Pro). Booting up into each OS is very smooth. I’ve installed several identical program in both OS in the same directory to save space and increase usability (I guess). All of them are smoothly installed and fully functional.
Problem arise during uninstallation process. Some program (not all) can’t be uninstall in one OS (ie Win98SE) after I’ve uninstalled them in the other OS (ie Win2000 Pro and vice-versa). I have to reinstall the program (in which OS it was corrupted), and then, uninstall is possible.
Are there other practical solutions for this situation or any tips to avoid this install/uninstall mess?