Why does my MBP 15 in. i5 Retina flash blue sometimes?

I've been using this computer as a general video and photo workhorse for around...maybe 2 years. I got this MBP retina within 2 months of its' release. Anyways, for the last few months, it does this weird thing where the screen flashes blue for a duration of between 1-2 seconds to 15 seconds. I notice it's much worse when running intensive programs, but I'm not running it any harder than normal. It happens especially when I bump the areas to the side of the mouse pad, where you would rest your hands when typing. I'm pretty sure it's a hardware thing. It doesn't have any problem booting, and other than the workflow interruptions it doesn't otherwise affect the computers performance. It happens often, though, and will happen every time I bump it. I've looked up blue screens, it's not the blue screen of death. Sometimes, when I'm feeling ansy, I tap the crap out of the sides of the mouse pad and when the screen returns to normal it says that my Hard Drive was not ejected properly. When I check, none of my hard drives that were plugged into the USB ports were force ejected (FCPX would have had to reload the projects and events.) I'm wondering if it has to do with the on-board HD.

Hi troy0891,
If I'm understanding your question correctly, when your MacBook Pro wakes from sleep, the internal keyboard and/or trackpad are slow to respond. However, in your comments, you mention a bluetooth keyboard finder launches.
Since your internal keyboard and trackpad are not bluetooth devices, I think this may be the issue. In the resource below, take a look at the section I have highlighted, and see if deselecting the option to allow Bluetooth devices to wake the computer" resolves your issue.
OS X Yosemite: If your Mac won’t go to or stay in sleep
https://support.apple.com/kb/PH18596?locale=en_US
Check your system’s Bluetooth settings:
Bluetooth devices can wake your Mac. If you don’t want a Bluetooth keyboard or mouse to be able to wake the Mac, choose Apple menu > System Preferences, then click Bluetooth.
Click Advanced, then deselect “Allow Bluetooth devices to wake this computer.”
If that option is already deselected, try turning your Bluetooth off if you are not working with a wireless keyboard and mouse.
Let me know if that helps ...
- Judy

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Please read this whole message before doing anything.
This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.
The purpose of the test is to determine whether the problem is caused by third-party software that loads automatically at startup or login, by a peripheral device, by a font conflict, or by corruption of the file system or of certain system caches.
Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards, if applicable. Start up in safe mode and log in to the account with the problem. You must hold down the shift key twice: once when you turn on the computer, and again when you log in.
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http://support.apple.com/kb/HT3964
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Why does my MBP 15 in. i5 Retina flash blue sometimes?

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