Evomattnc is right. Basically, if you have a modified app, it's going to have a different signature than the app provided by the developer. As such, you can't just install over the app. It's designed like that so that you don't end up with a hacked app. Naturally, you're using a different one on purpose, but you'd have to uninstall the existing one first. If it exists in /system/app, it can normally be upgraded by installing a new version to /data/app, and using it over the /system/app one. Naturally, the same signature rules still apply. You have to fully uninstall the existing one, whether it be in /data/app (normal uninstall) or in /system/app (by renaming it, just to be safe).