Computer delay...

Since upgrading from Leopard to Lion I am now experiencing a recurring problem I have never had before with this imac. At random points, with random applications running, a random action will cause the spinning wheel to appear as if the computer is doing something else before it actions what I've asked it to do. When this happens I have to just sit back and wait sometimes for up to 5 minutes for it to "catch up" and do what I've asked it to do.

It can be clicking on firefox in the dock when I'm in Photoshop or when I'm trying to hide inDesign to access the finder or even switching from the music to video tab in iTunes when my iphone is connected. Last night I couldn't shut the machine down because I hadn't quit out of every application I had running... It happens both when my time capsule is connected and not connected, when my phone is connected or not connected and when my ipod is connected or not connected... Seemingly totally random. The only thing that seems to cause it is that I'm asking the computer to do something different than it was already doing...

Once it happens it gradually gets worse and worse till every movement of the mouse causes the spinning wheel to appear. I can't force quit applications, I can't re-start, I can't open something else; it's like it's taking time to catch up with my previous requests.

I've used disc utility from my OS disc and it says the disc appears to be fine, I've verified and repaired permissions and I've downloaded all available updates.

This has only started happening since I upgraded and on several occasions now I've been forced to manually re-start with the power button resulting in the flashing question mark. I've then had to wait a few hours, try again and then it starts up fine...

Can anybody give me any idea why this might be happening and suggest anything I might do to correct it. Any advice would be grealy appreciated...