First off, you said they are different which really, they are not, not at all. If you install and update from a fresh install its no different then buying a newer copy. Next is you tried it on two different systems, which I can only assume are different, and as such unless they are identical to the last detail the argument becomes invalid.
They were the exact same system, with the exact same specs, age, software, and hardware. The only difference was that one was running a much older copy of Vista than the other one.
Another thing I notice, it may not emulate perfectly, but it does so without a hitch, unless the program is calling for some library that is not there, with which with most modern software from the past 4 years or so you should have no issue.. Now that you want to bring up DOS, if you knew anything about 64bit software and the OS that runs it, you would know you cannot run DOS programs in 64bit because its a 16bit program that is not and has never been supported, unless you use DOSBox which is a different story.
I didn't say that it wouldn't work, but neither did I say that it would work with everything. For example, there are several old video games that I play that cannot be run on a 64 bit system, despite not being DOS based, and instead being 32-bit software that does not require libraries that have been outmoded. The first is a racing game known as POD, the second an artificial life simulation known as Creatures, and there are several others, such as a sidescrolling shooter known as Hunter Hunted. (I play quite a few older computer games that even need to be set up in compatibility mode on XP, and might not work on Vista. Others include Pharaoh (outdated libraries), Caesar III (Just old), Star Trek Pinball (DOS based) and Wipeout (Outdated libraries, some versions are hardware locked))
You seem to know partial information of what you speak, however as a person who is in IT, I can tell you either were told, learned or picked up a lot of false information and are simply misguided. I mean no offense, not even with my first post, however as the OP is wanting proper information I see it fit to correct you as needed.
Are you going to reply to the comment, or just comment on my apparent misinformation? I have, in my experience, worked with one Vista computer that would not run RMXP, despite the fact that it had worked fine on the same computer in the past, and that refused to let me fix the issue. Killing all irrelevant processes, uninstalling all unnecessary software, rolling back updates to drivers and software, none of it worked. The only way I finally got it to work was to actually reinstall the OS.
There are different ways of doing the same thing if you read the sticky, all of them deal with making RMXP run as Administrator. Turning off the pointless, annoying UAC is the easiest way. RMXP works without any issues if you even remotely know what you are doing and use the latest 1.02a version of it.
Did you notice that the last one was a solution for those who couldn't get the program to run with administrative privileges alone? It may be touted as the solution to installing with no internet, but the original reason I dug through the registry for those keys was because some people just could not get the program to work, despite setting the proper compatibility and privileges to everything.
I've done my research here. I was the first person to post a method that almost universally allowed people to get RMXP working on Vista, and I know what I'm talking about. There may be some reasons that you might overlook for the difference between a new copy of an OS and an updated one, like the fact that the updated one is more fragmented by default, possibly has more files and registry entries that are remaining from before updates, and may actually be different for various other reasons as well, such as the installer packages and history for the updates that were installed.