Some things to check -
1) Does driver show up in Win Device Manager for Miniprog and no errors shown ?
2) Power on board match project settings ?
3) Silicon ID in project match what programmer trying to acquire ?
Make sure that exact part number is selected in Device selector (Creator option) including Engineering Samples name in the part no.
If you are facing issues with programming from Creator, try programming from PSoC Programmer. If you still face the issues, then take a screenshot of the PSoC Programmer settings and attach it here.
I believe that I have damaged my CY8CKIT-001 by trying to get miniprog3 to acquire the port, using either PSoC3 or PSoC5 modules. should have come to forums sooner. Miniprog3 showed as unconfigured in win usb devices. Visual device id, (cycling LEDs) did perform ok. Error code dbg.M0039 - "There was an error running port acquire. There may be no devices attached or a device maybe in use by another application" occurred after left-clicking on Miniprog3 device, system very sluggish. I should have looked into unconfigured miniprog, (but it worked for PSoC1 module). Thanks if you can offer help.
On the -001, you also need to make sure the settings for the power source (Vbus vs. Vreg) matches with how you power the board (power supply vs. USB). And also check that you connect the MiniProg3 to the PROG header on the PSoC module, not to the TRACE header. (I did both things wrong last time :(