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After much trial and tribulation, I was able to get a design with several UDB counters and USBFS to route properly. All Capture interrupts are occurring all the time, on a PSoC 5, along with using USBFS.
The key was to generate all of the timers and the rest of the design first. After that, you can add the USBFS to the mix, and everything works.
If the USBFS was placed into the design first,then there were clock skew issues, and the input clock to the counters could only be about 12 MHZ.
Also, if you want to debug faster and you are also using any fx2 based usb device, do the design in PSoC creator 3.3 or 4.0. 4.0 is much slower than 3.3, but 4.1 is glacial under certain circumstances. However, the user interface to setting up the USBFS device is *much* better in PSoC creator 4.1.