In general, see Files Not Syncing.

First, though, try the latest 4.0 Branch dev XPI. There's a bug in 4.0.4 that's preventing certain file sync errors from showing up. You may need to do a Reset File Sync History (or add a file from another computer) to trigger the redownload with that.

Did you try the branch XPI? Sorry if I was unclear—I meant that you might need to do Reset File Sync History or add a file with the branch XPI.

In the Sync pane of the Zotero preferences, do you have file syncing for that library set to "as needed" or "at sync time"?

Thank you very much, Dan. I installed branch XPI, but I'm not clear how to "add a file with the branch XPI". Do you mean to add one object from a website while having branch XPI installed?
I'm not using standalone.
It's not yet syncing my pdf database. My library is not a small one I think, it's about 2.2G. Could this be a network problem?

No, I meant add a file from another computer, sync that computer, and then sync with the branch XPI on this computer. You need to trigger file sync downloading, but Zotero skips the download step of file syncing if the last-sync time on the WebDAV server hasn't changed, and it updates the last-sync time after uploading a file. So you can either add a file from another computer or just do Reset File Sync History from the Sync->Reset pane of the Zotero preferences, which ignores the last-sync time.

Same here. I use Zotero Standalone in iMac/Mountain Lion and Laptop/Windows 8, and Cloudme for webdav syncing of files.
I followed your instructions as well but nothing happened. Exaclty the same behaviour as erjimenezpe. I can get the files from cloud.me, but they do not sync with my laptop.

Hello Dan.
Debug ID: D138679036 for an attempt to reset sync. Already submitted

Also, what's the timestamp for the zotero/lastsync file on your WebDAV server (assuming the file exists)?

I believe this is an issue with cloudme.com:

(3)(+0000000): HTTP PUT https://webdav.cloudme.com/[...]/zotero/lastsync

[...]

(3)(+0000001): HTTP GET https://webdav.cloudme.com/[...]/zotero/lastsync

(3)(+0000390): HTTP GET https://webdav.cloudme.com/[...]/zotero/lastsync
succeeded with 200

(3)(+0000001): Last successful WebDAV sync was Thu Jan 01 1970 08:00:00 GMT+0800
The server appears to be returning an incorrect date for the file that Zotero uses to track the last time a file was uploaded (in order to know whether it should bother downloading new files).

Could you load that URL (replacing the stuff I stripped out) in your browser, view the page info, and look at the modification time? (In Firefox this is Tools -> Page Info and the "Modified" field—the process will differ slightly in other browsers.)

Alternatively (or in addition), you can download the latest 4.0 Branch dev XPI and generate another Debug ID for a regular sync (no need for a reset), which will include that information. (If you do this, make sure you get version 4.0.5.r11266 or later. If not you may need to clear your cache in Firefox.)

Actually, that Page Info part was a bad test—in the absence of the Last-Modified header, I think that just shows the contents of the Date header, which should be the time at which the page was loaded. Are you sure you're seeing the sync time and not just the time you loaded the page? If so, I suspect cloudme.com is just returning the last-modified time in the wrong header. According to your latest debug output, the Last-Modified header appears to be empty.

If you want to confirm that that's the case and that this isn't an issue in Zotero, you can install the Live HTTP Headers extension, open it from the Tools menu, and then load the lastsync URL. You should see a request section (with a "GET" followed by the lastsync path) and a response section ("HTTP/1.1 200 OK") immediately below it. I'd be curious to know the values from the response section of the Date header and, if it's there, the Last-Modified header, and how they compare to the lastsync file's timestamp as you see it on the server.

I forgot to refer that I use box.com

D390660925

https://webdav.cloudme.com/[...]/Documents/zotero/lastsync
GET /[...]/Documents/zotero/lastsync HTTP/1.1
Host: webdav.cloudme.com
User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64; rv:20.0) Gecko/20100101 Firefox/20.0
Accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
Accept-Language: en-US,en;q=0.5
Accept-Encoding: gzip, deflate
Connection: keep-alive
HTTP/1.1 200 OK
Server: nginx/1.1.19
Date: Wed, 17 Apr 2013 01:36:00 GMT
Content-Type: text/plain;charset=UTF-8
Content-Length: 0
Connection: close

Hello, Dan.
This is the value from HTTP header, wed, 17 Apr 2013 01:36:00 GMT
Then I opened folder on cloudme.com, the lastsync is 2013-04-17 09:49.
BTW, I'm in China, cloudme.com seems to be providing my local time, and http header a GMT time. Seems that this is right, because, I opened cloudme.com minutes later.
I don't know, kind of confused.

OK, so it looks like this is indeed broken on cloudme.com's end (and perhaps box.com's as well). They're not returning a Last-Modified header for that file, which Zotero relies on to determine whether to try to download new files.

I've worked around this in the latest 4.0 Branch dev XPI, changing the way Zotero determines whether WebDAV file downloading is necessary. If you could install that XPI, do a Reset File Sync History from the Sync->Reset pane of the preferences (or, alternatively, upload a file from another synced computer), and sync again, Zotero should start downloading files again. This fix will be included in 4.0.6, at which point you should switch back to that. (You can also leave Zotero in download-as-needed mode until 4.0.6 comes out.)

OK, great. Thanks for your help debugging this. When 4.0.6 comes out (which should be within a day or two), remember to switch back to that.

Great! Seems to be working properly now. Thanks a lot for all your nice work!