Photoshop :: CS6 Windows Version Shortcuts

I am using Windows 7 OS, running Photoshop CS6 standard 64 Bit, 12GB RAM, dual XEON 2.6ghz processors. I am experiencing problems with shortcuts. I also experienced the issues when using the Release candidate.

The issues I have:
The shortcuts will work intermittently and appear to be effected when using the layers palette. The issue relates to  things like pressing the J for clone or B for brush. Sometimes they work sometimes they dont. Other times I get a chime noise/beep sounding when pressing the [ ] keys to increase the brush size. the brush will increase/decrease. The fix is normally to select the tool with the mouse and all is well for a while
 
I seem to have found a pattern when this occurs - and is when I have been using the layers palette. An issue I can reproduce. For example I duplicate a layer, then select the new layer - add a blending mode then click on the new layer, old layer and try the merge shortcut - nothing happens. Sometimes I get the chime noise as well but still no merge. If I click off the layers palette and then attempt the above - the merge works perfectly.
 
Equally if I attempt the merge of the layers without first clicking off the layers, and try to select say B (brush) I get the chime and the tool is not selected. Other times no chime and the tool is not selected. Again using the mouse to select it works ok
 
What was an inconvenience is a real pain now, as I am slowing down to do the click off layers trick or double checking the tool is the correct one I am trying to use.
 
Things Ive tried/figured out:

Ive ensured the kit Im running is technically sound and is not being created by a performance issue.I can reproduce this fault on different computers (all windows) I have tried resetting the workspace and removing all but the layers pallet, but the issue remains Ive even replaced the keyboard!! Even though the keyboard only has an issue in Photoshop.When running CS5 I did not have this issue, but the RC and the final version of CS6 displays this feature Ive closed all apps, with the exception of CS6 Photoshop to work out if is was an incompatibility - feature remains Seems to be related to using the layers palette, when not using the palette .