Hi Dan, I've just developed the same problem. I decided to my debug output to what Erika has said so as not to have you chasing loads of threads. I hope that's the right thing to do.

Anyway, I get the Invalid Output from Server notification. Here's my debug output from where things seem to go wrong (sorry about the page breaks: I don't know how to get rid of them:

[DEBUG REPORT EXTRACT]

zotero(3): Reloading all items

zotero(5): SELECT itemID AS id, key FROM items

zotero(5): SELECT I.*, COALESCE(CASE (SELECT COUNT(*) FROM itemCreators IC LEFT
JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=ITCT.creatorTypeID AND ITCT.
itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND primaryField=1) WHEN 0 THEN N
ULL WHEN 1 THEN (SELECT lastName FROM itemCreators IC NATURAL JOIN creators NATU
RAL JOIN creatorData LEFT JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=IT
CT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND pri
maryField=1) WHEN 2 THEN (SELECT (SELECT lastName FROM itemCreators IC NATURAL J
OIN creators NATURAL JOIN creatorData LEFT JOIN itemTypeCreatorTypes ITCT ON (IC
.creatorTypeID=ITCT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID
=I.itemID AND primaryField=1 ORDER BY orderIndex LIMIT 1) || ' and ' || (SELECT
lastName FROM itemCreators IC NATURAL JOIN creators NATURAL JOIN creatorData LEF
T JOIN itemTypeCreatorTypes ITCT ON (IC.creatorTypeID=ITCT.creatorTypeID AND ITC
T.itemTypeID=I.itemTypeID) WHERE itemID=I.itemID AND primaryField=1 ORDER BY ord
erIndex LIMIT 1,1)) ELSE (SELECT (SELECT lastName FROM itemCreators IC NATURAL J
OIN creators NATURAL JOIN creatorData LEFT JOIN itemTypeCreatorTypes ITCT ON (IC
.creatorTypeID=ITCT.creatorTypeID AND ITCT.itemTypeID=I.itemTypeID) WHERE itemID
=I.itemID AND primaryField=1 ORDER BY orderIndex LIMIT 1) || ' et al.' ) END, CA
SE (SELECT COUNT(*) FROM itemCreators NATURAL JOIN creatorTypes WHERE itemID=I.i
temID AND creatorTypeID IN (3)) WHEN 0 THEN NULL WHEN 1 THEN (SELECT lastName FR
OM itemCreators NATURAL JOIN creators NATURAL JOIN creatorData WHERE itemID=I.it
emID AND creatorTypeID IN (3)) WHEN 2 THEN (SELECT (SELECT lastName FROM itemCre
ators NATURAL JOIN creators NATURAL JOIN creatorData WHERE itemID=I.itemID AND c
reatorTypeID IN (3) ORDER BY orderIndex LIMIT 1) || ' and ' || (SELECT lastName
FROM itemCreators NATURAL JOIN creators NATURAL JOIN creatorData WHERE itemID=I.
itemID AND creatorTypeID IN (3) ORDER BY orderIndex LIMIT 1,1) ) ELSE (SELECT (S
ELECT lastName FROM itemCreators NATURAL JOIN creators NATURAL JOIN creatorData
WHERE itemID=I.itemID AND creatorTypeID IN (3) ORDER BY orderIndex LIMIT 1) || '
et al.' ) END, CASE (SELECT COUNT(*) FROM itemCreators NATURAL JOIN creatorType
s WHERE itemID=I.itemID AND creatorTypeID IN (2)) WHEN 0 THEN NULL WHEN 1 THEN (
SELECT lastName FROM itemCreators NATURAL JOIN creators NATURAL JOIN creatorData
WHERE itemID=I.itemID AND creatorTypeID IN (2)) WHEN 2 THEN (SELECT (SELECT las
tName FROM itemCreators NATURAL JOIN creators NATURAL JOIN creatorData WHERE ite
mID=I.itemID AND creatorTypeID IN (2) ORDER BY orderIndex LIMIT 1) || ' and ' ||
(SELECT lastName FROM itemCreators NATURAL JOIN creators NATURAL JOIN creatorDa
ta WHERE itemID=I.itemID AND creatorTypeID IN (2) ORDER BY orderIndex LIMIT 1,1)
) ELSE (SELECT (SELECT lastName FROM itemCreators NATURAL JOIN creators NATURAL
JOIN creatorData WHERE itemID=I.itemID AND creatorTypeID IN (2) ORDER BY orderI
ndex LIMIT 1) || ' et al.' ) END) AS firstCreator, (SELECT COUNT(*) FROM itemNot
es WHERE sourceItemID=I.itemID) AS numNotes, (SELECT COUNT(*) FROM itemAttachmen
ts WHERE sourceItemID=I.itemID) AS numAttachments FROM items I WHERE 1

zotero(3): Releasing session lock

zotero(3): HTTP POST version=3&sessionid=******** to https://sync.zotero.org/unl
ock

zotero(3): <?xml version="1.0"?>
<response version="3" timestamp="1233919586"><unlocked/></response>

[COK DEBUG REPORT ENDS]

All the best,
Ciarán

I'm not sure that that can be the problem Erika: I'm getting it on a WinXP machine with 3.0.5 installed, but was getting the error before the update. Plus I was getting the error last night on my ubuntu box too, which hasn't upgraded yet. My guess: this error means that we've fouled up our server-side database in some way. Only a guess mind.

I upgraded Firefox and am getting the same error. Also imported some references from another zotero database.

I also noticed that the reset preference pane is impossible to get to work. It fails and pops up a window saying you need to enter username and password on the other tab even when the username and password are already there.

When I removed the recently added collection, I still get the invalid output from server error (new data never got to server as far as I can see). The error is generated on an XP laptop which upgraded Firefox this morning. My OSX iMac which upgraded Firefox yesterday, seems to be synching zotero just fine today - no error messages.

So, at least for me, the server side error seems to only effecting the XP version of of zotero SP.

Thanks- it all works perfectly now

Cheers

Sorry, forgot something: Syncing at home on a private PC or Mac is no problem. The error only occurs at the university (on three different pc's we tried) so maybe it is a university-network related problem?
Erika

ok, no new build of zotero since 3.6
so, thought about it some more
the items that are not synching (most are) appear to be pdf files that i dragged into zotero subcollections without first creating an item and attaching.
these appear on the original machines library, but do not synch across to others
so, maybe you need to manually attach each pdf to an item created in zotero?
i've been doing this mainly to keep copies of unsorted reprints on the server for later updating, assuming i will do pubmed searches later, create an entry in the appropriate collection for each reprint, and then attach the pdf to the detailed reference

just curious whether the drag and drop of pdfs into the zotero window should create items that synch across platforms. its a nice feature if so, but seems to not be creating synch-able entries.

cheers!