I have recently experienced a lot of serious problems with various Astronomy software on the Mac since upgrading to OS X Mavericks. I have not figured out whether there is an impact on EQMac, but my opinion is that it could definitely adversely affect at least pulse guiding. Here is a link to an article I posted on the issues and how to work around the problems. I will be releasing an App Nap aware version of EQMac as soon as I can find the time. In the meantime, you should follow the advice here.