Thunderbold with Macbook pro 13 some programs doesn't function properly

I have a macbook pro 13 early 2011 that I connect to my thunderbold 27 display. The problem I have is that some programs don't function properly. For instance, in the doxy pro software I can't select any of the options under(over) the send menu option. I see the menu and everything, but when I hold the mouse over one of the options it doesn't become highlighted. If I try to move the application over to the laptop display by draging it I can't "release', i.e. it sticks to the mouse pointer The only way to get out of the situation is to kill the software. This is not the only software that acts funny, Eclipse IDE is also affected.
Cheers,
Kungalm

Try this:
Reinstalling Lion/Mountain Lion Without Erasing the Drive
Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.
When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the main menu.
Reinstall Lion/Mountain Lion: Select Reinstall Lion/Mountain Lion and click on the Continue button.
Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.

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