Still, that doesn't sound good. I have no idea why that would be happening to you at all; that install routine's IBM authored, and all I can say is that it worked here.
It won't affect any "third party" programs you have, like moz or netscape; they only interact with mpts. It's mostly a question of whether you have a complete set of tcpip apps installed or not.
Can you see if it left some kind of a log?
Do you want me to email you a file listing of my \\tcpip\\ folder, to compare with yours?