Quite simply MS put out a special disk for the change over from 98 to 98 SE if you have the 98Se disk it won't upgrade you have to do a full reinstall. However if you can get a copy of the upgrade disk it will perform the upgrade with out any problems and MS did give quite a few of these away at the time as I have 5 copies here that MS sent to me without any explination.
But idf you put a 98Se disk into a computer loaded with 98 it will autoload and tell you that the CD contains a newer version of Windows do you want to upgrade? If you click on yes it will start to look at your system and do a bit of examination and then tell you that this version of Windows is not compatable for the job and to obtain the correct version it should give you the part number of the upgrade disk. But if you simply can't get your hands on a upgrade copy the only option that you have is to reinstall Windows from scratch but if you installit over the top of your existing version of windows you will lose all your settings but at least you will retain all your data but you will have to reinstall any device drivers that Windows doesn't reconise or have in its libary.
In this case your best bet would be to back up all your data {good pratice anyway} andthen wipe the drive and perform a clean install as it will work better anyway, you will have to reinstall all your software as well and then restore your data but that way you will get the system working as well as it can. But the important thing here is don't forget to log onto Windows update site and install all the updates particuarly the security ones as if you are using the internet you will need these.
