Lightroom not using the Monitor Profile

I have recently set up a new computer with a new monitor. When I got PS and Lightroom set up on the new system I noticed that when viewing photos in both applications the colors are VERY different compared to how they look viewed online or in another photo viewer from my desktop (windows 8). I also noticed that when I opened PS I got a message saying that the Monitor Profile is "bad" and I could opt out to ignore the profile. When I did ignore it the color looks fine. Blacks are black, gray's are gray, etc . . . Anyway, I am wondering if there is a way I can have Lightroom ignore the profile as well. I have a monitor calibrator and I will try that, but I am wondering if it will do anything only because other applications look fine. Hope someone can shed some light on this!

First of all, Photoshop and Lightroom are fully color managed applications that will actually use the monitor profile to display the image.Many other applications (viewers/browsers) are not and will just ignore it. So there's a difference right there.
That said, when you get that message in Photoshop, it means exactly what it says. That profile is bad and should not be used.
The real solution is to use a calibrator to make a new custom profile for your monitor. Until you get that up and running, use sRGB IEC61966-22.1 as monitor profile. You set this up in Control Panel > Color Management > Devices:

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