Project folder not behaving-not remembering changes

Running OSX 10.8.5 on a 2.26GHz Quad-Core Intel Xeon.
I have a project folder that should consist of 19 different sub-folders displaying in icon view and is locked. All folders are very organized. If I have three folders that are called folder 1, folder 2, and folder 3, they are displayed in that order from left to right folder 1,2,3. Prior to having 19 sub-folders I had 17. Everytime I needed to make a change I unlocked the main folder and did the changes. Then locked it again ( for accidental deletion ). This is the second time in a month that this folder is behaving and displaying the contents prior to having 19 sub folders, back when it had 17 and the folders that are named folder 1, folder 2, and folder 3 are now displaying folder 2, folder 1 and folder 3 also before re-organizing the main folder. The main folder is located on a secondary drive not the main boot drive. I ran disc utilities and everything checks out. Thankfully I did back-up the main folder. But from then till now the work was not backed up. I believe I only lost a little work.
What is causing the folder that is not located on the main HD drive to behave this way?
Did I get hacked, bug, trojan etc.?
Tomorrow when I wake up it will probably be back to normal. What gives?
Should I be concerned about the drive? Or something else from the system?
Thanks.

anyone?

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