Digital Neg Not Same Size As Original...

What I mean by that is, the printed out inkjet negative, when laying it on top of the in-camera negative, it is off by a few mm, in both directions. I've never noticed this until now. I've checked to make sure that no resizing is happening, and that it should print the negative at 100%. I was as careful as I could be at the scanning end of it, in that I was telling the scanner to only scan the negative, and not the area outside, via frame lines... Any ideas?

Go through the chain and see where things start to shift around. You know the scanning resolution so compare the scanned image dimensions and calculate those back to mm based on the dpi of the scanner and see if there's a difference there. Then do the same for the print. There's probably a small error in both steps. Perhaps if you post some numbers we can work out what the likely culprit is.
But this is a fundamentally challenging issue; it's not you!

I've measured the actual size of the negative, and made sure that that jives with PS. Scanning rez also jives with PS. It's weird...

Can you post some numbers? I.e. a small image of the scan with some information of which dimension you've measured and the pixel dimensions of that section of the full-size scan.
What printer do you use? What print settings?

Just a weird thought...

Some printers have a setting for expanding an image slightly. This is used to ensure that there are no thin white border when one prints a borderless image.

You would hope that this would only be applied when you actually tell, the printer to make a borderless image. However, this may not be the case. Stranger thing have happened with software!

Thus you might try to disable this feature of the printer driver even though you are presumably not printing borderless.

As I said, an off the wall thought but stranger things have been known to occur .

I have found when printing separation negatives through print tool if I put one separation on the canvas vertically and the other horizontally I will see a discrepency in size.
Also if the image size is too close to canvas size you will find some clipping occurring which may change the size.

I'm a new user of Print tool and suffered the same issue with the negative being a few mm smaller than intended size. I found out this was caused by adding the image file but it was wrong orientation for the page setup. Having rotated the image so it showed correctly on the page, I noticed that in the 'Position and scaling' section, it was showing 97.4% instead of 100%. Changing this figure to 100% then gave the correct size negative. I too got the clipping warnings. Rotating and saving file in PS stopped the issue too.