btw: my setup is this:

I'm using zotero 4.0.15 in firefox 25.0 on Ubuntu 12.04

There's a ton of output in there, since it looks like there's an active sync going. Assuming this still happens in 4.0.16 (which is likely), temporarily disable auto-sync and then provide a Debug ID for just a single save attempt from Google Scholar that doesn't go to the right collection.

Possibly unrelated, but it also looks like there are some issues with various attachments in your library. Items NX8R3WAN, PBXBKKQ2, R4DFJRAW, UNBIFFKJ, UDSW56KD, WKPGPDG3, and WNC4JUSW (and possibly others) all show as having symlinks in them, which should never be the case under normal operation, suggesting that you're doing/using something weird. You can paste those keys into the Zotero search bar (in "All Fields & Tags" mode) to see the attachments in question. For the ones that have their files locally you can do Show File to see the symlinks. Some of those attachments might only exist on another computer or online, though, in which case you can check on the other computer or view them online with URLs like https://www.zotero.org/drevicko/items/itemKey/NX8R3WAN. Zotero isn't currently able to properly deal with symlinks, so you'll probably want to just delete those from zotero.org, but it'd also be good to figure out how they got into your library in the first place.

what was your problem exactly? You can just drag&drop items to copy them to collections in Zotero.

The first symlinked thing (NX8R3WAN) is a web page item and shapshot. The item is acutally a download URL via a proxy: http://ieeexplore.ieee.org.virtual.anu.edu.au/stamp/stamp.jsp?tp=&arnumber=1541280

Probably a red herring, but if I recall, something weird was happening with the web proxy... I was viewing the page for an article over the proxy (from home), right-clicked the pdf link, then chose "save to Zotero" - this didn't work. When I clicked the link, I got an "unauthorized" HTTP error, and I don't think the url was going through the proxy. I can't remember how the web page item appeard (can't check right now as I'm in the office and the proxy doesn't work here).

The second symlink thing (PBXBKKQ2) is an ordinary pdf attachment. On my work machine, all local copies are not symlinks (I have webdav setup for zotero on my work machine too - not symlinks in that either). I believe the long trace came from my machine at home though - it's just possible my firefox profilea at home is symlinked? Can't check right now, as that machine is turned off..

I tried the link in your comment (Dan) and it comes up with the web page item ok, nothing seems wrong. I can even click the link, and (here in the office, where the proxy removes itself) it downloads the pdf.

And if the pane is open, are you in a normal collection, or something like a Unfiled Items or a search?

I had the zotero pane open and a normal collection selected (not a search or a special collection like Duplicates or Trash).

I just did another one (D184971235) - restarted firefox and made sure only one instance of zotero was running. I selected a collection (before turning on logging), then logged saving a reference from google scholar - it went into "My Library".

I have zotfile installed, so some of the trace will be renaming the pdf.

disabled all addons except zotero and Ubuntu ff modifications and restarted ff: D1608633528, D797311069

Steps:
1 - launch firefox (it loads the previous session, but only content from visible tabs, zotero was not open in the previous session)
2 - open zotero (opens as a tab)
3 - select a collection (it's actually a sub-collection of another collection)
4 - enable logging
5 - click folder icon in g.scholar tab address bar
6 - popup appears asking which articles to save
!! at this point, it already says "saving to My Library"
!! there are only 3 lines reported as logged
7 - select the article I'm interested in
8 - wait for it to finish (all popups disappear)
9 - click "submit log to zotero"

I did this twice, just to be sure (the t logs above)

Is there another way I can ask zotero via chrome: about which folder is currently open? Perhaps I can track such a request??

ok, here it its: D1864937808
I noticed that selecting the collection logged 94 lines, then clicking the folder icon in the address bar logged 3 (already it said "my Library")

open zotero (opens as a tab)

Does it happen in the pane view?

(already it said "my Library")

Where? Don't paraphrase. I assume you mean it says "Select which items you'd like to add to your library"? If so, that doesn't mean anything — it says that for everything, including group libraries.

(the full message is in the above post under step 6)

Ah, sorry, missed that. Hmm, yeah, that should show the collection. I'll take a look at the debug output (but also try disabling the Ubuntu extension).

@msmole - any further questions please post to a new thread, since it doesn't sound like you have the same problem, but it does seem like you're misunderstanding how collections work:
http://www.zotero.org/support/collections_and_tags?&#collections

Another trace with Ubuntu extensions (and everything else) disabled:
D175974201

I used a different translator: http://eprints.lancs.ac.uk/1433/

Dan: "Saving to My Library" appears in the little notification pop-up in the bottom right of the window at step 6 above. The google scholar translator pauses at this point with a second popup asking which articles to save.

It's been a busy time, and I haven't had a chance to get to this.

I noticed just now that on my mac (running zotero in firefox), things go into the open folder ONLY when the zotero tab is in the same window as the tab with the item(s) I'm adding.

If the zotero tab is in a different window, the item goes into "My Library".

I thought this might be related to having zotero open in multiple windows, but I tried relaunching firefox and opening zotero in only one place, and the behaviour was the same. Firefox does, however, reload my tabs (though it only actually loads the ones with focus), which may be restoring something hidden related to zotero? I had made sure zotero was not open in any tabs when I relaunched firefox.

I suspect that's the problem all along! When next in my ubuntu setup, I'll try there.

Excellent! I'd say the problem is solved! (:

Makes sense when multiple zotero tabs are open. I just checked, and zotero won't open a second tab in the same window.

I guess the confusion is from zotero open in only one place - a naive user may expect different behaviour. But it also makes sense to have the same behaviour when only one zotero tab is open (for consistency - otherwise even more confusion ensues!)

Perhaps a note should be added to the FAQ? At least one other has had this confusion, and likely many more.