Missing files on external hard drive and unable to delete items in trash

When my external hard drive is connected I am unable to eject it because it says it is in use. I have tried shutting every program, but the message still occurs. I have also noticed that I can't empty my trash can when the external hard drive is connected, and that it appears empty when it is ejected. There are also missing folders on the drive. I am able to see the timemachine backup folder, but I can't open it properly to access the data.

With the External HD connected to the AEBS, I went to File -> New -> Folder and named the folder. I had done this a few times, as well as created a few new ones using Picasa and cutting/pasting them into the appropriate folder. I did that a few times. Then one more time I went to File -> New -> Folder on the EHD (not Picasa), named it and hit enter. I got a message saying can't do it because folder doesn't exist. Properties showed correct amount of GB used/remaining. so I know it's there. Latrer I connected directly to PC and folders were there and could be manipulated. I tried reconnecting EHD to USB hub in AEBS and it won't show up as a drive under Computer, but under Network -> <AEBS name> -> drive name.

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    Here is a very good writeup on de-fragging in the OS environment that I borrowed
    From Klaus1:
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    http://support.apple.com/kb/HT1375  which states:
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    Mac OS X 10.2 and later includes delayed allocation for Mac OS X Extended-formatted volumes. This allows a number of small allocations to be combined into a single large allocation in one area of the disk.
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    VKP90 wrote:
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      If you always follow that rule that should be written in stone, you'll never be sorry.... (and I know countless 1000s that have been)

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