I agree. I initially thought it would be tolerable, but e.g. when I want to (re-)tag a file and bring up the tagging window, I'll usually look for the tag that I want to change first, and only then click into the window (at the right position, of course). In effect, that workflow is to bring up the window -> search -> click on the field I want to change. The flashing, though, forces me to click into the window at a random location, because otherwise, it distracts me so I have to re-start searching. Not only does this necessitate further action (which can be a nuisance, depending on how many other things I'm doing at the moment), it also brings with it a focus change, which means I have a higher chance of accidentally altering values that I actually wanted to leave alone, without noticing, or perhaps noticing too late.
Add to that the peculiarity that I'm never 100% sure that I actually sent a click somewhere (I blame the touchpad I'm currently using), and being able to turn off pane flashing becomes a really nice prospect.