Today we released Foxmarks 0.59. If you've got a large set of bookmarks (or a not-so-fast PC), you'll want to upgrade to this version, especially if you've noticed a "mini-hang" while Foxmarks was doing its work. This latest version attempts to chop the overall synchronization process into a sequence of chunks, none of which should take longer than 1/10th of a second to execute.
It also fixes a long-standing problem that has tripped up many users: in previous versions, Foxmarks was unable to know that you had imported bookmarks, so imported bookmarks would not sync properly. This is now fixed.
Give it a shot, and let us know what you think.