The way that the IDE captures the output from external processes is a bit problematic. I took a look at it briefly and did not see a trivial fix. If I do look at it again I might refactor it. A lot.
The problem with fixing these sorts of problems is that the easiest way to make the problem go away is to put the debugger on it, or add some logging! This is what the verbose setting sometimes magically solves things.
So it requires someone who really want to bite into it, and who can reproduce it. I'm not quite the former (yet) even if I'm the latter. Another problem is that I mostly use make at the command line to make sketches now, so I have little personal incentive to improve the IDE. Yes, a terrible excuse, but what can you do?
But, I will try to take a look at this one this week-end. Like I said, I think there will be a fair amount of refactoring to do, so it may take awhile to get right.