Files are automatically placed in trash, ***?

Hi,
This is an issue that has been troubling me recently. I find that OS X Automatically places files in the trash can, such as the app file for my kindle for mac and also a video editing software I need to use quite often. I have also found mixes and sound files that are integral to projects that I am working on and completely irreplaceable.( These are of course backed up elsewhere).
HAs anyone come across this before? And can anyone tell me how to remedy this very, very irritating issue?

This mysterious disappearance happened to me yesterday, although nothing to do with Kindle.
I'm on a Mac Mini (2010) with Snow Leopard and was working on InDesign (CS5), when it crashed and vanished. Nowhere to be found. Since all the support documents were still in place, I just copied the app file over from my backup drive and it worked fine. Then, hours later, Photoshop & Illustrator disappeared....so I started up MacKeeper. I then noticed the trash needed emptying, but thankfully looked in it first. There were all my missing apps, plus other apps I hadn't even missed yet (iLife apps, Activity Monitor & lots of support documents. Odd things like the Painter brush collection).
Couldn't find anything online about this, other than people have been experiencing it since around 2009 (Snow Leopard debut?) but no one had a clue as to its cause or remedy.
I'm always surprised when Mac techies say they've "never heard of....." some problem before. Is anyone starting to hear about it now? There is little discussion about it, I admit, and it took a while to find the right keywords to get anything.
I placed my trashed files back in their respective locations, took off "admin" priviliges after reading that Apple recommends this, and ran some utility apps. I then backed up my HD to a different external drive, in case there was still something wrong--didn't want to ruin my good BU drive. All is fine so far, 24 hours later.

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