Well it turned out that the problem was being caused by a corrupted desktop file. The TCP/IP icon and anything to do with TCP (such as prefs) were all affected and seemed garbled. A quick check with ResEdit showed that there was nothing wrong with the files themselves.

Strangely enough it was a spontaneous restart (my IIcx does that occasionally) that solved the program as the System automatically re-build the desktop file.

It's a bit odd though. I'm going to keep my eye on it and see if it happens again.