I found an error in the portal.js (well really its in script.js) that was preventing the saving of the collapse state of portal blocks. In portal.js find:
elk_setThemeOption(sp_sides[id], mode ? 0 : 1, null);
elk_setThemeOption(sp_sides[id], mode ? 0 : 1, null, null);
and
elk_setThemeOption("sp_block_" + id, mode ? 0 : 1, null);
elk_setThemeOption("sp_block_" + id, mode ? 0 : 1, null, null);