Your iCloud is on the fritz.  Assuming that all of the bookmarks you want are in BookMacster, and your Home folder is backed up, try this…

• In BookMacster, check the Syncing button in the toolbar.  If it sports a green dot, click it to Pause syncing.
• Click the BookMacster menu and verify that near the bottom is a disabled menu item Stop Workers (0), Agents (0).  This indicates that you have 0 active Agents.
• In Safari, click in the menu: Bookmarks ▸ Show All Bookmarks.
• Delete all bookmarks.  (You can also do this by exporting an empty document from BookMacster.)
• Wait a few minutes.
• You might also need to clear out your bookmarks in other Macs or iOS devices in your iCloud.  It also sometimes helps to switch off syncing in System Preferences ▸ iCloud ▸ Safari  (Bookmarks in 10.7) for a few minutes.
• Keep deleting bookmarks, etc. until you can leave it for 20 minutes, with iCloud Safari/Bookmarks syncing switched on, and no bookmarks.  It can be helpful to launch Activity Monitor and filter for a process named SafariDAVClient.  Whenever SafariDAVClient is at work, that means that iCloud is working on your bookmarks.

Starting from a clean slate, you should be able to re-enable syncing and export from BookMacster.  Let me know if you have any more trouble.  Your other thread means that something may have gone wrong recently.