I am not sure what you mean by your IBSTA window, but the behavior that you describe is familiar. When I was doing some GPIB programming for a customer, I thought that this was just one more effect of my not yet knowing quite how to program it right. But I did get it working, so here are two guesses as to what you might need.
Do you have the latest drivers?
When you know about the CMPL indicator, you see it displayed somewhere, but does your program also know about the CMPL indicator? If your program hasn't resynchronized with the driver, then the driver has to assume that the program still considers the operation as being in progress, and maybe it can't discard buffered data.