Should the find window not come up as the default file collections folder when you're searching within it? For example, I've set up a new file collections folder and copied files into it and did a cntrl-F. Instead of the default search field being my file collections folder, it's the last folder I chose to do a find on (which wasn't a file collections folder). This seems like a bug - running 9.0.0.9.
Also, I just did a remove files from file collection option. They went away no problem, then I did a cntrl-z and I got a warning saying that deleting a file from the file collections folder will delete the real file. I did a cancel and my files seem to still be there (whew) but this also seems like a bug. The cntrl-z operation should've put the files back in the file collections folder, I would think ...
Sorry for the triple, this one may be in the user manual. What's up with the #1 in the "name" column (I'm using details mode) inside my file collections folder. It hangs around and seems to stay #1 even inside sub-directories. When I click on it the column sorts by name and it goes away and it doesn't seem to come back after that ...
One last note on file collections, I promise. 
I don't think you should even have the option (directly at least) to delete files in the file collections folder, that's just downright dangerous. It's too easy to screw up files in multiple folders. If you must have a delete option (not the remove files option but the delete which could delete files on networked folders not covered by a recycle bin) then it should be buried one or two levels down with no default hotkey for it or anything.
Just my opinion.
Please ask separate questions in separate posts, otherwise we end up with spaghetti threads that nobody can follow or work out whether all the questions are answered yet.
Some answers:
[ul][li]Searching within collections doesn't work properly at the moment and that's why you get some other path if you open the Find panel while viewing a collection.
[/li]
[li]Numbers in column headings appear when you are sorting by multiple columns. You're probably sorting by Name-then-Location or something like that. (Ctrl-click on column headers to sort by more than one column.)
[/li]
[li]I think the real bug/issue is that when you remove something from a collection it is not added to the Undo list at all. When you pressed Ctrl-Z afterwards some other operation was undone instead. I've reported this to GPSoft.
[/li]
[li]Deleting the real files from collections is a useful and very common thing to do. For example, people often do a search for particular files (e.g. *.tmp) which they then want to delete. You get a warning message before the delete happens and the message looks different enough to others that I think most people should read it, so I don't see that it's so dangerous that you could justify removing such a commonly used feature.[/li][/ul]
This is still apparently broken in 9.1.0.0.
For now, it seems that the only choice is to either type the path to the collection manually (yuk!) or drag-and-drop the collection onto the Find window (as long as it's not covered by the Lister). It's easier to DND to the Find panel, but I generally prefer the window.
Is that an accurate summation, or am I missing something obvious again? 
-Jeff
I don't think anything has changed in 9.1; finding in Collections still isn't really supported.
So the best option might be to flatten a folder view, filter it by and then perform a Find on the flattened, filtered list?
There's no need to flatten the view before running the Find. Find is always recursive. (Well, unless you clear the Search inside subfolders checkbox.)