I don't particularly like how kopete utilizes notifications to remidn me of new ims. Often times I'll miss messages from friends because they'll be buried beneath a bunch of other system notifications once i get home. i much preferred the taskbar specific notifications in pidgin or empathy. however i can't seem to get it to work that way even when i disable pop up notifications and only enable task bar notifications in the notifications settings. does anyone have any advice?

or perhaps can someone tell me how to set kopete such that it doesn't hide the initial IM?

Have you checked the Notification settings in Kopete itself?
Open Kopete > Settings > Configure Notitications.

I noticed my taskbar didn't have a Message Indicator widget. Strange but that definitely made things infinitely better.