Can My New Hard Drive Be Causing Back-Up Weirdness?

Last week, I bought a new Seagate 100GB/7200 rpm HD, which I've been using externally in a Firewire enclosure. I wanted to try it out for a week before I install it into my Pismo.
I've been using computers for 20 years, and I'm conscientious about saving often, and backing up everyday. Here's the weirdness: Today, Saturday Oct 6, I opened the two files I've been using every day, only to find I'd lost two day's work. I checked the Last Modified date, and sure enough, both files were marked Wednesday, Oct 3. So, I checked my internal HD to which I've also been saving my work. Same thing. Both files marked Wednesday. So I checked my memory stick. Same thing. Both files marked Wednesday.
The most likely explanation for this is no doubt user error of an all too common kind but I am, as I say, extremely careful about backing up. So today, when I'd finished, I saved both files, and closed both files. I checked them in the HD's list, and they were both marked with today's date. Fine. So I clicked and dragged the first one over to the folder in the Internatl Drive. No problem. It alerted me that there was an older version and did I want to change it. I did. That went fine. But then, with the second file (also marked Today), when I dragged it to the Internal Drive's folder I fumbled it slightly, and I got a message saying "THere is a NEWER file with that name in this location." Huh? Sure enough, the file in my target folder was marked Today, and now the source file was marked Wednesday again!
The order I've been saving things is first to the new external HD, then to the internal HD, then to the memory stick (although I only used the stick on Friday).
First question. Is it possible there is something wrong with the new HD that would cause this? I don't want to install this puppy if that's the case. In fact, I'd want to return it.
Second question. If I've saved a file but haven't closed it, and then drag its icon from the HD to another target, will I be making a copy of the latest saved version? Or only the latest CLOSED version? (I don't think I did this yesterday, but it's possible, I guess).
Third question. Even if it is human error, what error could I possibly have made that would lose TWO days work and not just one?
Thanks for any light you can shed on this.

Thanks JPL. At least now I know I'm not going mad. The drive really did undo what I saved. I watched it happen again on the weekend (but this time I'd emailed the work to my Yahoo account before I copied it in any direction). But it's still pretty unnerving to see it happen.
What you say accords perfectly with what I've been reading on the Panther forum and elsewhere. I didn't know anything about jumper settings. I looked up Toshiba (re the old drive) and Seagate (for the new drive) on the subject. Both are remarkably confusing. Toshiba's settings are dependent on whether "Pin 28" is High or Low, but they don't explain what this means, nor which pin is 28. Seagate's illustrations do not resemble my new drive and they contradict what is shown on the label.
Unfortunately, I went ahead and put the new drive into the machine set to Cable Select. And re-did the whole SuperDuper process. But after reading the above sites, I decided it should probably be set to Master. So I opened up the Pismo again and reset it (that only took about 5 minutes). I am just now completing the SuperDuper process again.
I also checked OWC's Help Desk and you're right--they say, "All drives should be set to Master when used in a FireWire case. If it is a dual enclosure then one is set to Master and the other Slave."
So it seems all this rigmarole stems from the HD having shipped set to Cable Select, since both the Enclosure and the Pismo want it set to Master.
Clarification: do you mean I should now re-initialize the old HD which I've now put into the Firewire enclosure? I haven't changed its jumper settings. I'd like to avoid SuperDupering again, if possible, as it takes over an hour. Wouldn't I just be cloning from the clone I just made?

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    The order I've been saving things is first to the new external HD, then to the internal HD, then to the memory stick (although I only used the stick on Friday).
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    Second question. If I've saved a file but haven't closed it, and then drag its icon from the HD to another target, will I be making a copy of the latest saved version? Or only the latest CLOSED version? (I don't think I did this yesterday, but it's possible, I guess).
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