Please enable logging (Configure --> Options --> Logging Enabled) and restart PT3. Then reproduce this slowdown and attach the ~/Documents/PokerTracker/PokerTracker.log file to a support ticket and we'll investigate further for you.
Maybe it is actually PS itself that makes the problems. When i close PS my ram gets to 1.9GB free, and when PS is running for awhile it comes down to 11mb free or so
Try zipping it up and let me know how small it gets down to. The max we allow uploaded is 5M but text compresses extremely well so it's possible that will actually get down small enough.