I had a similar issue recently, Re-installation allone did not help.
So I de-installed ALL Cypress's Programs (Creator, Designer,Programmer)
Then I freed all USB-devices (Free program USBDeview) Re-boot
Then downloading latest Designer 5.2 and Creator 2.1 and installing (complete), that helped.
I uninstalled previous versions and installed the latest, I used the program that I recommend the usb and uninstalled all the usb, but when I configure the 2.1 psoc creator gave the message: Warning: dbg.M0039: There was an error running port acquire . There may be the devices attached, or the device may be in use by another application "and does not constitute giving psoc programmer busy and soon fail.
I would suggest you to create a technical case
Support -> technical support -> create a case
It seems some drivers are messed up. What version of Windows do you have?
Sometimes deinstalling will not completely remove all drivers.
1) Try uninstalling PSoCProgrammer and disconnect all Miniprog3.
2) Try Microsoft Cleanup Utility (if you can find, otherwise let me know) to see if any traces are left.
3) Check if the CyMiniProg3Service is removed from services.msc and check if CyMiniProg3Service.exe isn't running.
4) Reinstall PSoCprogrammer.
Oh, and don't forget to check the devicemanager on yellow exclamation marks. Repair the drivers if any problems are noticed...
I also had a very similar problem.
I was using Miniprog 3 to program a PSoC 5 device.
My PC went to sleep, (not standby) and when I woke it up the miniprog was locked out with the same issues you see.
In my case nothing would resolve it apart from a reboot. I thought at the time that it was a problem with the powermangement section of the miniprog driver.