Do LR4's random metadata warnings mean something serious?

Question

(LR4.1 on a 2011 iMac with 16GB RAM, running OS 10.7.4)
I am doing my first big job in LR4, and am worried by the way that metadata conflict warning flags (of two types: 'Error writing metadata' and 'Metadata was changed externally') are appearing and reappearing randomly on my image thumbnails. There is absolutely no consistency in which images are affected. I imagine the problem may be caused initially because I used to apply a couple of presets on import - a copyright line, and also camera-specific Develop settings. These were created in Lightroom 2: most of the 14,000 images in my Lightroom catalogue predate my upgrade to LR3 in October (I went to LR4 at the end of April, and 4.1 a week ago; I didn't notice this problem in LR3, but I didn't do much work in that version of the program, so it may have been present and I just didn't notice).
As I say, not all images are affected; but those that are have nothing particular in common. (Whereas most of my photographs will have had the presets applied on import, or else later - when I came up with the new camera-specific defaults, I also applied them retrospectively to all images I hadn't yet processed individually.)
My frustration is not just that this problem exists in the first place: if it is caused by the import presets, I've deleted the develop one (and triple-checked that nothing other than Lightroom's own processing defaults is being applied), and recreated the copyright one, throwing the original away. However, when I try to clear the flags, by clicking on them and OK'ing the dialog box, or doing command-S and OK'ing that way, they sprout up again either immediately or soon after; sometimes on the same images as before, sometimes on other ones.
I've got 'automatically save to XMP' checked as a preference (have had for years, so all my images have XMP files beside them). Although Lightroom imagines the images have also been edited in another program, the vast majority are NEF raw files, and I don't use any other image viewing or editing programs. (There are also a few Photoshop files that may or may not have flags.)
How I've tried to solve it:
1. Doing lots of saves - either selecting all the images in a folder or collection and doing a manual save or clicking the flag and OK'ing the dialog box; or selecting only the images affected and doing the same; or going through one by one, ditto. But whatever I do, more flags sprout on the same or other images in the folder (although sometimes after several saves, they seem to vanish for good).
2. Throwing LR's preferences away. Since this made no difference, I retrieved and reinstated them.
3. Deleting all user presets in Develop, plus the copyright one for Import. (I do have Print and FTP presets, which I hope I don't have to throw away as well. I'm not using those modules at the moment, though.)
4. Realized there was no point on optimizing the catalogue, since that happens automatically, alongside checking its integrity and backing it up, every time I quite Lightroom - which I do after every work session, to ensure I'm fully backed up.
5. At some point in all this, I also restarted my Mac (after I'd deleted the preferences, I think).
6. I have excluded the LR catalog from my Time Machine back-ups, although there was an interruption to this for a few days this week, after I upgraded to LR4.1 (and now I'm worrying that in fact this might date back to my upgrade to LR4 in April). But presumably the catalog isn't corrupt, or I'd get a warning during the regular checks on its integrity?
What's really worrying me, is that this weird behaviour means that there's some instability in Lightroom that'll mean the work I've done on my images is compromised in some way, and I'll lose it.
How can I get rid of these random (incorrect) warnings permanently?
(I did post on this last week, but didn't realize how pervasive and peristent the problem was. I rang Adobe for support on 7 June and got cut off twice; they haven't responded to the case they opened when I was cut off the second time. I tried phoning them three times this morning, and couldn't get through - I was cut off again, twice; the other time I just got dead air. Their phone system seems to be completely up the creek. When I did manage to speak to someone, the sound kept going - which the techie seemed oblivious to, no matter that I kept telling him I couldn't hear him.
I'm really worried that the intensive work I'm doing in Lightroom at the moment will all go to waste, so I'm holding back when I really need to take advantage of the few days I have free right now to do the work.)

Answer 1

Thanks, everyone, for your suggestions.
John: I back up the catalogue (and optimize/check its integrity) every time I quit Lightroom - which is why excluding it from Time Machine isn't the end of the world. I did rename the catalogue early on in my troubleshooting process - as you say, I didn't like the fact I felt out of control of it.
I tried synchronizing a folder that had some flags: when I'd done there were three flags in the folder. (I have unclicked - and clicked and then unclicked - the 'unsaved metadata' checkbox in View Options: as I say, Lightroom shouldn't be displaying these flags at all.)
Rob: Thanks for understanding why I'm fretting! I've checked my XMP sidecars, as you suggest, and they have read and write privileges. I then checked the last-modified date on the XMPs that came up with flags after I'd synchronized that folder. One of them displayed the time I'd just synchronized the folder (it's one I haven't worked on apart from applying a blanket preset in LR2, and then a blanket update to PV2012 in LR4, as I've done to all the images I haven't yet worked on individually); the other two showed the time (I presume) I worked on them yesterday. I selected these three and applied command-S: they then showed, correctly, that they'd been modified a minute before. So far, that folder's now flag-free. (As I said in my original post, the flags sometimes do seem to vanish if I save enough times - and they're unpredictable, not necessarily appearing on the same images in a collection or folder as before I do I group save/clear conflict.)
Mollysnoot: I don't see how the Mac OS would be doing this (although who knows - I'm not a software expert). I don't have any other programs open that can modify images. And since these flags can reappear instantly when I've dealt with the conflict - before I've had time to take a breath, even - I don't think they represent any actual modifications.