Links to MOV files from PDFs don't open in Safari

I have a website that loads PDFs to the user's browser. In the PDF are links to Quicktime MOV files which open floating windows in which users can see videos. These work fine in both Firefox and Windows Internet Explorer on both of my Win 7 64-bit PCs. And they work in Safari on my son-in-law's Mac laptop, which runs OS 10.5.8, although not in Firefox on his laptop. The symptom is that the PDF (or browser) does not seem to even know that the cursor is positioned on a link; that is, the cursor does not change to a pointing finger as it should, and of course clicking on it has no effect.
On my desktop G4 (867 MHz), booted to OS 10.5.8) the links are also not recognized as such (no pointing finger) in both Firefox AND Safari (version 4.0.2, although the download package claimed it was installing 4.0.5). Or rather the icon I downloaded claims to be Firefox, but appears merely to point to a Mozilla web page. So I suppose we don't know about Firefox. What we can say is that Safari 4.0.2 on my Mac G4 PowerPC tower with 10.5.8 booted functions like Firefox on my son-in-law's Mac 10.5.8 laptop - unawareness that the links even exist.
Booting in OS 10.4.11 (which I can do from another hard drive on this G4 Mac), I have different problems. Firefox does load there (version 3.6.8), and goes to the main html page on the website. When links to the PDF files in that html page are clicked on, a choice between Acrobat Reader 7.0 and Acrobat Reader 9 is offered, but only Reader 7 will open - or claim to open: actually, although the title of the page is correct, all I see is a blank page.
The PDFs do open in Safari (version 4.1.3) on this G4 booted to OS 11.4.11, and the links in the PDFs are recognized as such, but when I click on them the little Multimedia Player Finder window comes up, telling me I need to download the correct media player, even though Quicktime 7.6.4 is sitting just below on the dock, and opens the identical MOV files with no problem directly from the hard drive itself (actually a different hard drive, but wait...yes, it also opens fine when the MOV is copied to the hard drive on which the currently booted OS10.4.11 resides).
Okay, so when I click on Get Media Player in that little Multimedia Player Finder window that opens when I try to go to a MOV link, I'm taken to Apple's website, which offers to download Quicktime Player 7.6.9 for Leopard. Drilling down to the appropriate version for Tiger 10.4.11 and downloading that, I find it knows it should install that to the same hard disk on which 10.4.11 resides, forsaking all others. Good. But when I install that and Restart, it's the same story as before: the PDFs load from the website into Safari, but when I click on one of the links in those PDFs to a MOV file I get the same Multimedia Player Finder window saying the media requires an additional player.
Can anyone shed any light on these problems?
Thanks in advance for your help.

>With Perian you just goto System Preferences>Other Row, right click or Control+click on Perian, choose Remove Perian Pref Pane.
That sounds like Perian is NOT one of those you can just delete. How does one know which is which?
>But Perian would only help if you want to display the movie in the Browsers.
In fact, due to issues of publisher's permission regarding about half the video clips, for the present I would prefer the user  NOT to be able to download them, but only to be able to open them in the browser, or even better, in a floating window that's a child of the browser, as I specified to Acrobat, and as in fact happens on my Win 7 PCs.
>Do you need PDFs to be downloaded, or could you do this in HTML and have the Movie links right on the site?
I'd rather they NOT be downloaded, at least in the sense of winding up in the Mac's Download folder and opening in a separate window. I want them to open directly in the browser window, as the do in my Win 7. (MOre on this below.)
As to HTML instead of a PDF, what I need is to be able to provide commentary about each video clip, which HTML could do just fine, and I could get free of the VERY troublesome problem that any time I make more than a trivial change to the text, I must re-link every stinking one of the MOVs in a time-consuming process. So far, however, all of my attempts to show video via the <OBJECT> or <EMBED> tags have either failed, or opened the clip directly in the page, not in a floating window as I prefer. I believe there's a new <VIDEO> (or is it <MEDIA>?)  tag in HTML 5 I may look into.
> Check System Preferences>Accounts>Login Items window to see if it or something relevant is listed.
Also look in these if they exist, some are invisible...  /private/var/run/StartupItems; /Library/StartupItems;
/System/Library/StartupItems; /System/Library/LaunchDaemons; /Library/LaunchDaemons
Thanks much for this tip. Indeed Protools itself is in the System Preferences>Accounts>Login Items folder, and I'll be removing it from there, but I'll still have the 'In use by another application' problem when I load Protools as a conscious choice. There's a bunch of Digidesign (a.k.a. Protools) stuff in /Library/StartupItems, but ... (I was about to say I would investigate further because Protools is notorious for placing files all over the place and not have a clean uninstall, but I just realized these are StartupItems  - meaning, I suppose, *boot-up* items, as opposed to any time one starts up Protools? If only boot-up, there should be no harm in deleting them.
>I don't think that is any part of the problem.
Thank goodness! Just guessing: can I assume that (in principle, at least) any app from a prior OS Applications folder should run in a later OS, but generally not vice versa? That's the default assumption in Windows. However, I know of at least one app I have that was written for OS 9 and they announce does not run in higher OS's, though to be honest I've never tried it.
>The problem seems to be that the ones that do not display the links, or display the links but won't play it, are looking for the Movie file in the Download folder. No expert, but I kind of think it's some MS "stanrd" involved, which Apple trys to keep pace with, but...
I'm convinced you have the right answer here  - except perhaps for the Microsoft part, because the 'Cannot play media because file not found' problem also occurs in Foxfire on my two XP PCs (although not in Internet Explorer where everything works properly on those two XP PCs). The evidence that you're right? I noticed an instance - TenFourFox when booted in 10.4, I believe  - where not only the links to the MOV clips have that problem, but also links from within one PDF to another PDF, which generally *were* working in most scenarios tested so far when the MOV clips were not. For what it's worth, the links to the other PDFs specify another folder on the server, while those to the MOV files specify no folder at all since they're all in the same folder as the PDF that links to them. Which is why the Mac assumes they must be in the Download folder. Depending on the situation, apparently, in some circumstances if you do specify a folder Mac figures it must be on the server if not found locally.
In general, the problem seems to have a lot to do with browser configuration issues, including security, but I don't know what. Perhaps related, perhaps not: Every time I try to load a PDF in TenFourFox it asks me what app to open it with and I have to specify Acrobat Reader. I have found no way to load that as a plug-in (and even if I did, how to tell TenFourFox it should use it). The Get Add-on dialog lets you hunt for plug-ins but neither Acrobat Reader nor Quicktime show up when you ask for them in the Search box.
But now... guess what?
Today, suddenly, when I access the site with Safari while booted in 10.5.8, EVERYTHING IS WORKING! All the clips open, and they open in floating windows just like I want. This, remember, is the situation in which the links were not even recognized earlier. I have no idea which if any of the changes we've discussed could have brought this about. I've not even been able to find out how to tell Safari it should be using Acrobat Reader and Quicktime. But somehow, it is! (I'm not making this up, nor, despite my admission of memory lapses on occasion, is this a case of a memory lapse. I described this situation early in my initial post, when I had just verified it.)
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