For now, you'll have to just disregard issues that Kabuto continues to report. Regarding the application crash trigger, would a "white list" of sorts work for you? As in, you could tell Kabuto that it's "ok" for certain applications to chronically crash?
Regarding the hard drive capacity and the red eye - I'm sure we can come up with something to give you control over the notification icons as they appear in your Devices table. We don't want to clutter the dashboard with configurable notification settings, but we don't want to mess with our users' OCDs, either! I'd bet that the rate of OCD symptoms among techs (and RepairTech employees, for that matter) is a bit higher than average