When you press S or CTRL+C you now get a selection box with 1-pixel acuracty, but really it only selects particles with a 4x4 block alignment. This means the selection box no longer correctly shows which pixels are being captured. Please fix this bug.

It's not a "placing stamp" problem. Your description applies to placing stamps.

It is a "SAVING stamp" problem. The box edges no longer correspond to the outermost pixels which will be captured. Some times the box edges don't even fall on a 4x4 block correctly, and you MISS pixels that you thought you were going to capture!
Also the outer edge of the box doesn't correspond to the mouse cursor's position. Instead it correspond's to the mouse cursor's position - 1pixel.

The real problem is it didn't used to be have this way. The selection box USED TO automatically jump to the nearest 4x4 pixel boundary, so you always knew by just looking at it, how many pixels would be selected. I found that MUCH more useful.

You can reposition AFTER you start the stamp pasting process but before you finalize the paste, by using CTRL+arrow. Someone showed me this once and it made obsolete any possible changes to the saving system that I'd previously suggested. DEVS PLEASE MAKE THE NEXT VERSION LIKE THE OLD WAY OF DOING THIS! I got so used to the old way that I simply made sure to select a bit more than I wanted. Now with change (which was so ackward I for a time actually belived it was a BUG in the beta version, until it actually made it into the release version) I find that it is SO DIFFERENT from the previous way stamp saves were made, that now for me TPT is practically UNUSABLE (so much so that I've considered not ever upgrading again, even if it means missing out on new elements that are released, as at least the older versions of the powder toy were at least USABLE, but this new thing basically BREAKS the software for me when it comes to me using it, not sure about how it effects other users).

This crap about a selection box with 1-pixel accuracy is an example of one user suggestion that should be made into a mod, and ONLY a mod. There's pleanty of times I and other people's suggestions that got replied to with "that's never gonna be official, if you want it, make a mod with it". Well this crap about 1-pixel accuracy selection box for stamp saving is one idea that should NEVER have been in the official version. It was a clear oversight on the part of the developers to NOT reply to such an idea with "sorry guys, this'll only ever be in a mod, NEVER an official feature". The devs NEVER should have considered this abomination for an official release. They should have thought how people (such as myself) who use the TPT might be NEGATIVELY EFFECTED by it.

Some elements might break saves, but this feature breaks the usability of the WHOLE GAME for me (and I believe many others may feel the same way, but don't have the courage that I do to directly confront the game developers with their grievances).