Wake up unresponsive

I manually sleep my Mac Mini when I leave it for an hour or two. It's often unresponsive when I wake it up. The desktop looks normal, but clicking with the mouse (wired) produces an odd pop up menu, not the function I clicked on. In fact, I can get no chosen fuction to work by clicking anywhere in the dock or in a window. The top screen menu functions do work, including restart. Restarting the computer clears this issue, but it's been happening more lately, and getting really annoying.
Has anyone seen and resoved this problem?
Thanks in advance.

At this point I think you should get Applejack...
http://www.macupdate.com/info.php/id/15667/applejack
After installing, reboot holding down CMD+s, (+s), then when the DOS like prompt shows, type in...
applejack AUTO
Then let it do all 6 of it's things.
At least it'll eliminate some questions if it doesn't fix it.
The 6 things it does are...
Correct any Disk problems.
Repair Permissions.
Clear out Cache Files.
Repair/check several plist files.
Dump the VM files for a fresh start.
Trash old Log files.
First reboot will be slower, sometimes 2 or 3 restarts will be required for full benefit... my guess is files relying upon other files relying upon other files! :-)
Disconnect the USB cable from any Uninterruptible Power Supply so the system doesn't shut down in the middle of the process.

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