Usually that means that the program, which is not in your working sample rate natively, did not have enough time to finish the SRC. In the Master settings you should see one called RATE_CNV, you'll want to set that up some. Many third party devs recommend setting it to about 3000 which should be enough for most programs. If you ever need to you can always jack it up further.
I have had my RateCNV up to max for months now, and I have never noticed any negative side effects, but have also never had the sample-rate change issues I had before I set it. So win for that suggestion!