It sounds like you're doing everything right - and you should be able to add/modify the program used by Konqueror at will. Here's what I know:
1. Konqueror uses the standard KDE file associations.
The KDE documentation page for setting up file associations is here:
2. On my system (and, it sounds like yours):
a) I happen to be running the KDE desktop (not GNOME, for example)
b) I go into KDE Control Center | KDE Components | File Associations | Application Types | x-zip
The filename patterns are *.zip and *.ZIP.
The Application Preference Order is "ark"
On my particular system (Suse 10.x/64), ark happens to be on the path, in /opt/kde3/bin/ark.
c) I can [Add] new file types; I can [Add] new file associations, and I can [Add] new Embedding services (whatever the heck that means ;-))
3. Finally, I imagine I could manually edit local options in my $HOME/.kde directory, or global options in my /opt/kde3. For example:
cd /opt/kde3/share; grep -i ark * */*|grep -i zip 2>/dev/null
Again, the root directories are probably SuSE-specific - but the general principles should be the same for any distro.
'Hope that helps .. PSM