The 10px issue seems to be gone from my profiles so right now everything looks alright on my end as I fixed the other things by myself a couple of days ago. I just hope there isn't more to come now.
Gregorovitch is still misaligned by 10px, as are Harry J. Potter, Charlye, Tigrean and Kanis :(
I've not changed any of the coding for them for a while (trying to avoid changing any coding on there until I know for certain that there shouldn't be any more weird changes happening to them!)
[edit] Put into one post to make it easier for to be able to find the information without trawling through multiple posts.
It still looks misaligned for me, although others seem to see it as it's meant to look.
Browser: Chrome Version 40.0.2214.91 m (also tried Chrome Canary and Opera - no difference in any of those) Resolution: 1600 x 900 Cleared cache twice / restarted browser / tried hard refreshing - no difference
What I see for the pets I linked above: 
If it helps, adding in
{margin-left: 186px;}
seemed to resolve the layout misalignment (tested on Cybill's profile, using Gregorovitch's coding)....

Have you tried a hard refresh? Because for me the Pets you've linked here look just fine. :o
nods I've cleared the cache, done a hard refresh, and they still seem misaligned (Kanis, Charlye and Tigrean all have the story text over the left border, Gregorovitch's story background overlaps the main background image where it shouldn't, and Harry J. Potter's alignment problem is the hover where the Hogwarts badge is) o.O

I was able to spot the issue on Harry's profile (barely visible though) but the others don't seem to cause any issue on my end. That's really strange. o__O;
This is what I see for those profiles (cropped to show the 10px misalignments)
The .owner section on Gregorovitch's profile has also moved, as it wasn't overlapping the species before
....I could just recode them all, but I'm reluctant to do that until Keith is certain it's all back as it should be, as otherwise that could be a lot of profiles for me to change back again afterwards!

Looks really different then. o__O
This is what it looks like on my monitor: Click!
The red bordered part is the only issue I see on Harry's profile by the way, the alignment of his name / species info is perfect for me, too.
o.O that's exactly how they should look (not sure if I'd even spotted that bit on Harry's profile before or not) - that's really weird....

Now I'm afraid that only I can see my own fixed profiles as well. Would you be so kind to check the profile of Hypnos (leashed) for example? I know that his profiles was affected by the 10px issue until yesterday but today it looks fine again for me.
takes a look yeah, Hypnos looks like it's all 10px too far to the left (the story overlaps the box too) :(

@ Paddy
That's what I was assuming, seems the "fix" only affected a part of us, the rest still sees the errors...maybe based on browsers or screen resolution?
But thanks for checking, like you I won't fix it by myself now, did it with some issues before but it only took 24hours until the next thing broke so I'm going to wait and see what happens next. The fact that I currently see everything in perfect shape doesn't make it easier though. :c
thanks for checking mine too - at least if some people can see it aligned correctly, we're a bit closer to them all being right for everyone :)
I added all my info into one post so Keith can find it easily, just in case the browser / resolution makes a difference :)

That a good idea to add everything to a single post! Let's hope it'll help to finally find a solution for everyone. :)
Hmmm... the fact that different people can look at the same pet and see different things is really weird. Is there anything in the pet profile coding that should allow for relative viewing? As in, different screen sizes would look different?
This concerns me for when it comes to pet spotlight reviewing. Since we don't get feedback from the reviewer as to why things were rejected, if this issue isn't fixed, it could cause a lot of problems. Like, literally, for some people the pets look perfect, and for others they are still misaligned. And that's looking at the same pet.
In case this IS a browser/size issue, I just checked and I am using FF 35.0 and my screen is set to 1366x768.
When I look at Reserved, I see a huge space at the bottom that was never there before, but no alignment issues.

When I look at Najas, I see a misalignment, but no issues at the bottom.

So, I just noticed something when I was bouncing between tabs. For reference, I am using the shadowglen background. So, on most pages, there is a thin space between the edge of the window and the events bar on the far left side of my screen (about 10px). On a pet profile (one with NO css/profile), this gap is no longer present.

Could this be what is causing the alignment issues? Pretty sure that this is a new change? Just trying to think of stuff that might help/be the cause.
I also see a 1px black line running through both of the profiles you linked (which could probably result in a rejection, if the checker sees it too). This seems to be something only half the users on the site see (people running the same browser, some can see it and some don't).
That line is the most annoying thing ever, mostly because I don't understand why it's there in the first place nor do I get why only some people see it and others don't.
If you want, this should kill it for you though:
{border: 0px solid ;}
I think I can actually explain this one? I always use Shadowglen and never see that line. I changed my layout an hour ago, and then received your ping and doubled check... and using the Morostide layout, I now see the line! So, after going through all the layouts (except I don't have the Luminaire Hidden one), it seems that the black line only shows (for me using FF 35.0) for the Morostide Layout. Is that what you use? Maybe this is an issue with the layouts/that particular layout?