Yes, that's true, and it causes clicks as well, what is sometimes enoying when you are recording at the same time and need to go to Pulsar to fix something in the mixer.
I have that message in Logic when I switch to another application. The funny thing is that Logic is idle. I use it only for the EVP88 epiano, nothing else. I'd rather prefer it as a standalone instrument, but EMagic said 'nope, but the CPU load of the empty sequencer is neglectible anyway'.
I just click the box away and ignore it, but I find it annoying too.