One more - Sync doesn't work at all, my windows Firefox doesn't show any bookmarks made from my Linux FF.

On each device: Type about:sync-log in the Location Bar and hit Enter.

Take a look at the error logs. Copy and paste the lines for failed or unsuccessful processes.

1402054764863 Sync.Service DEBUG User-Agent: Firefox/29.0 FxSync/1.31.0.20140428193838. 1402054764863 Sync.Service INFO Starting sync at 2014-06-06 07:39:24 1402054764863 Sync.Service DEBUG Exception: Could not acquire lock. Label: "service.js: sync". No traceback available 1402054764863 Sync.Service INFO Cannot start sync: already syncing? 1402055666708 Sync.Status DEBUG Status for engine bookmarks: error.engine.reason.unknown_fail 1402055666708 Sync.Status DEBUG Status.service: success.status_ok => error.sync.failed_partial 1402055666709 Sync.ErrorHandler DEBUG bookmarks failed: App. Quitting Stack trace: checkAppReady/onQuitApplication/Async.checkAppReady()@resource://services-common/async.js:123 < waitForSyncCallback()@resource://services-common/async.js:98 < makeSpinningCallback/callback.wait()@resource://services-common/async.js:141 < _syncStart()@resource://gre/modules/services-sync/engines/bookmarks.js:376 < SyncEngine.prototype._sync()@resource://services-sync/engines.js:1477 < wrappedSync()@resource://gre/modules/services-sync/engines/bookmarks.js:214 < _sync()@resource://gre/modules/services-sync/engines/bookmarks.js:220 < WrappedNotify()@resource://services-sync/util.js:143 < Engine.prototype.sync()@resource://services-sync/engines.js:655 < _syncEngine()@resource://services-sync/stages/enginesync.js:199 < sync()@resource://services-sync/stages/enginesync.js:149 < onNotify()@resource://gre/modules/services-sync/service.js:1255 < WrappedNotify()@resource://services-sync/util.js:143 < WrappedLock()@resource://services-sync/util.js:98 < _lockedSync()@resource://gre/modules/services-sync/service.js:1249 < sync/<()@resource://gre/modules/services-sync/service.js:1240 < WrappedCatch()@resource://services-sync/util.js:72 < sync()@resource://gre/modules/services-sync/service.js:1228 < <file:unknown>

1402055666907 Sync.Engine.Passwords INFO 259 outgoing items pre-reconciliation 1402055666907 Sync.BrowserIDManager DEBUG _ensureValidToken already has one 1402055666908 Sync.BrowserIDManager ERROR Failed to fetch a token for authentication: [Exception... "App. Quitting" nsresult: "0x80004004 (NS_ERROR_ABORT)" location: "JS frame :: resource://services-common/async.js :: checkAppReady/onQuitApplication/Async.checkAppReady :: line 123" data: no]

Jay: the interesting part of the log is probably earlier than the fragment you posted, but if I had to guess, I'd say your bookmarks database is corrupt. That would explain the failure to save new bookmarks.

From that log, and your statement that your other machines can't see your bookmarks, it's apparent that bookmarks sync didn't get anywhere, so it's unlikely that it made any changes — and it wouldn't delete any new bookmarks in any case.

You might try the Places Maintenance add-on:

https://addons.mozilla.org/en-US/firefox/addon/places-maintenance/

and if that doesn't help, try quitting Firefox and moving places.sqlite out of your profile folder. Firefox will restore the contents from a backup, then Sync will run over the top.

I ran Places Maintenace, it said this:

> Integrity check - The database is corrupt > Reindex - Unable to reindex database > Integrity check - The database is corrupt - Unable to fix corruption, database will be replaced on next startup

Great! Restart Firefox, see if that gets you syncing.

Yes a restart did wipe my bookmarks, then they were instantly restored, I did lose my new bookmarks.

And the sync circle stopped rotating, a good sign.

I disconnected my windows FF and will see if it picks up any changes from my Ubuntu FF.