I did a couple quick tests and both windowed and fullscreen worked alright for me. What browser are you using? I used Firefox, haven't yet tried in Safari or Chrome.
My only problem was the graphics sometimes looked weird and distorted.
Look at the difference between switching from windowed to fullscreen:
and switching from web page to fullscreen:
I don't understand what would make that difference but changing fullscreen from 800x600 to 1024x768 under game options fixed the distortion in the second shot (and made it a good bit prettier too).
Also, the screenshots were darn near impossible to find and the "screenshot captured" text when you take it disappears so quick I had to take 6 shots just to read it all.
For myself and anyone else searching for screenshots:
(user) - library - caches - Panda3D - start - pirates_test - screenshots