Adam,

I appreciate your efforts. I agree, all my troubles seem related to the same problem. At this point (11:30pm PDT) I seem to be unable to even "Submit to Zotero Server". But here is the debug report (very short):

[JavaScript Error: "The character encoding of the plain text document was not declared. The document will render with garbled text in some browser configurations if the document contains characters from outside the US-ASCII range. The character encoding of the file needs to be declared in the transfer protocol or file needs to use a byte order mark as an encoding signature." {file: "zotero://debug/" line: 0}]

version => 4.0.8, platform => Win32, oscpu => Windows NT 6.1; WOW64, locale => en-US, appName => Zotero, appVersion => 4.0.8

=========================================================

(5)(+0000000): SELECT COUNT(*) FROM fulltextItems WHERE (indexedPages IS NOT NULL AND indexedPages=totalPages) OR (indexedChars IS NOT NULL AND indexedChars=totalChars)

(5)(+0000000): SELECT COUNT(*) FROM fulltextItems WHERE (indexedPages IS NOT NULL AND indexedPages<totalPages) OR (indexedChars IS NOT NULL AND indexedChars<totalChars)

(5)(+0000001): SELECT COUNT(*) FROM itemAttachments WHERE itemID NOT IN (SELECT itemID FROM fulltextItems WHERE indexedPages IS NOT NULL OR indexedChars IS NOT NULL)

(5)(+0000001): SELECT COUNT(*) FROM fulltextWords

(3)(+0003352): HTTP GET http://www.zotero.org/download/xpdf/Win32.latest

(3)(+0001448): HTTP GET http://www.zotero.org/download/xpdf/Win32.latest

....another example of not being able to connect: when I check for Zotero updates under "Help", it also doesn't connect. I am not aware of using a proxy, except once I am using the library (have not used that today and never logged into that proxy today). Do you have a suggestion where to look (Windows 7)? Thanks.

Adam,

Thanks for sending that tool. I am getting a few things to work now.

Here is what I am finding out:

The system-wide settings under "internet options" (oreilly link above) are the same that I see in the Chrome settings. In both, my "LAN Settings" are:

------------------------------
(checked) Automatically detect settings
(checked) Use automatic configuration script
Address: http://www.lib.ucdavis.edu/proxy/[...]
(NOT checked) Use a proxy server for your LAN
------------------------------

The automatic script (second check above)automatically offers me to login to the library proxy (for database access), but only once I arrive on the library webpage. Of course, that is how I get to my literature (and how I would like to operate with Zotero), but at the moment, the connection doesn't even work before I login to the proxy (or with Chrome just turned off).

Here is what I tried as a fix:

I "unchecked" the two "checked" boxes in my LAN settings (from Windows 7 internet options per the link you provided, http://answers.oreilly.com/topic/675-how-to-configure-proxy-settings-in-windows-7/). I did not turn off the Chrome browser. But I did have Zotero closed. I reopened Zotero. The result: the connection issue seems to be resolved (I will add these as I go through):
* Zotero properly checked for software updates
* it installed the PDF Indexing version ok (under "Tools - Options")
* it properly created a parent item from a pdf by reading its metadata
* it properly renamed the pdf
* zotfile now works properly

FYI. The connection issue is also resolved (i.e., working) if I "check" the first box ("Automatically detect settings"), but not the second box ("Use automatic configuration script"). The connection is broken (again) if I only check the second box [a simple check on "Help->Check for Updates" will reveal the connection issue]

here how i solved that problem, in windows 7, xpdfbin-win-3.03

1. download latest xpdf from http://www.foolabs.com/xpdf/download.html
2. extract the file xpdfbin-win-3.03.zip (latest today)
3. copy pdfinfo.exe and pdftotext.exe (check whether 64 or 32 bit os) into Zotero Data Directory Location,
4. delete pdftotext-Win32.exe and pdfinfo-Win32.exe in Zotero Data Directory Location ,
5. rename pdfinfo.exe ==> pdfinfo-Win32.exe and pdftotext.exe ==> pdftotext-Win32.exe ,
6. open zotero

the 3.0.3 version of pdftotext works with copy protected PDFs, the 3.0.2 version shipped with Zotero doesn't, so this may make sense under some circumstances.