I will like to know which brand Isolated USB Hubs you are using.
As going for isolated usb hub decreases the usb speed.
So please check the USB Speed of the Isolated USB Hubs.
I have heard of UHR307 Isolated USB Hub which are industrial USB Hubs, you can have a look at the data sheet of the same.
The hubs are:
1. Intellegre USB1072
2. Advantech UH/BB-UH201 (not so much a hub, but an isolator)
Can you try the following steps:
1) In PSoC Creator goto the debug tab.
2) Click on Disable All Breakpoints
3) Click on Delete All Breakpoints
4) Build the project and then try debugging or programming using miniprog.
Please let me know if you still face issue after following the above steps.