Thanks for your post. It is upsetting that "Always open in …" changes without help from the user. That should simply NOT be possible.
I think the problem must be in the 10.7 Finder, mostly because, commonsensically because there should be no way an application can affect icon placement. That's the Finder's job.
The system calls used by applications _should_ be exactly the same as before. It is difficult to accept that the pros at Apple wouldn't be very careful to maintain backward compatibility.
Here's an experiment I started yesterday: I left my HD root folder set for icon view with Arrange By… and Sort By… both set to "none" and I arranged the icons in my customary way, which puts the System folder at upper left. I closed it and I've been checking it periodically since then. At least once, maybe twice, I've found the System folder displaced all the way to top right of the window. All other icons seemed unaffected.
I tried to do some work yesterday and today, besides exploring this issue (<very sad grin>,) and here's what I observed, as briefly as I can:
Yesterday I opened a folder deep in my HD hierarchy, call it "Sam", a folder I have not opened for many months. "Sam" is part of a s/w app support library and it opened in icon view, apparently just as it was installed, no special icon arrangement, just a single row across the top of the window. I copied some files to "Sam" from another directory, "Fred". "Fred" was in icon view arranged according to my customary scheme. I noted that the copied file icons retained their exact source arrangement in "Sam". In other words, when I closed "Sam" yesterday, it was "correctly" arranged in icon view, two new rows below the original top row.
Today I navigated to "Sam" and found it was still "correctly" arranged in three rows just as when I did the copy yesterday. No problem.
I closed "Sam" and then a few seconds later, I re-opened it. The ONLY operation I did in the meantime is that I navigated to the next most enclosing folder, i.e., two levels up from "Sam", by using Go --> Enclosing Folder. Since I've got Finder set to "Always open folders in new window", both windows stayed open.
What I found in "Sam": Strangeness, as if .DS_Store has been corrupted. In icon view only some of the files were visible and I could neither resize or scroll up/down or left/right to view them all. In list view the left-hand column --the filenames-- was invisible, off-window to the left, and I could find nothing to correct this. After playing around for a while with no success I closed "Sam" and used Terminal to rename Sam's .DS_Store to "old.DS_Store". Then I re-opened "Sam" and all seemed OK… uncorrupted. In icon view my arrangement was gone. I tried several different views, leaving it in list view.
Minor additional strangeness: I noticed the renamed .DS_Store file wasn't visible. "old.DS_Store" should have been visible in the MacOS window but wasn't. I made a copy named "foo" -- no help. I copied it to "aaaaaa" on the desktop -- still invisible. Conclusion: there's more than meets the eye here, maybe an obscure or new "invisible" file attribute on top of the leading dot to make files invisible. Probably this isn't relevant to the current discussion.
Really staggering strangeness: After all this, I was preparing to try to reproduce the problem. Just for grins, one last time, I decided to check "Sam" in icon view. Yesterday's "correct" icon arrangement was back! Three rows and spacing, to the best of my recollection, just as I left it yesterday.
Yesterday's icon arrangement should not have survived my renaming of .DS_Store in that directory. And I did a lot of experimenting with the View Options settings first, which almost certainly changed the organization. Incredible! I cannot think of any reasonable explanation for the reappearance of the correct icon arrangement.
Here's a completely off-the-wall possibility: 1) 10.7 automatically saves backups of .DS_Store files, often. 2) The .DS_Store in "Sam" _was_ corrupted between the first and second time I viewed that folder today. 3) 10.7 is now capable of detecting the corruption and restoring .DS_Store from the last non-corrupt version.
If this is so (ha!) then people experiencing mal-rearrangement should be able to recover by immediately deleting (renaming) .DS_Store, but that doesn't seem to be what you or anyone else observes.
I can't even argue that the window problems I observed today are related to the icon mal-rearrangement issue at all, since the icons I could see were correctly arranged.
Sheesh.