Ahh OK, I assumed (there goes that word again!) that you grabbed it from the wiki link, which is pointed to the new one. Sorry!
Look, as I said, MIDI-Ox does work 99% of the time. Especially if you already know that your core, midi interface and java runtime are working 100%, it’s not a big deal. The thing is that the other 1% tend to go really really south, sometimes mysteriously (because it should not be possible to make it this bad) ending up in a need for reburning a PIC or even a new one, and almost always resulting in many hours of support time (doh)
In johnc’s case, if I were him I honestly wouldn’t bother changing back to MIOS Studio, because he has experience and lots of gear all working. Chances of being in the 1% are pretty low for him. In your case, however… 
Glad you like the forums man. The feeling is entirely mutual. Yeh the organ guys are hella helpful. They probably get tired of me always saying nice things about “the organ guys” 
Oops, new posts… Johnc, I’ll explain why I felt it necessary to voice my disagreement… but first: you should know by now that I’m only a moderator for janitor duties bud. It’s not like there is any “rule” that says <booming God-voice> “THINE SHALT ALWAYS USE THY ILLUSTRIOUS MIOS STUDIO WHEN UPLOADING” or “THY SHALT NOT COVET THY MIDI-OXEN!” </booming God-voice>:D Even if there was, I would have no involvement in writing or policing it. This whole thing:
There was a day, not long ago, when all questions, comments, suggestions, tips, were welcome on this forum, and the best help came from the user who was working his way through the process. Having been rebuked by the forum moderator, I will be a little less prone to put my two bits worth out there.
Is just a bit melodramatic That day is still here, and it will not ever go away.
Edit: now that I think about it that really is crazy talk. You feel like you shouldn’t voice your thoughts, because someone else voiced theirs, and it wasn’t the same? Does that mean the other person’s thoughts are unwelcome? You don’t seem to think so, but why do you feel that way about your own? Why should either opinion be exclusive? You kinda make out like my opinion has changed the forum forever, but not yours? Where’s the fairness in that? Should I keep m own opinion to myself so that the forum can have an environment where all opinions are welcome? That’s a paradox… The whole thing is layers of parodox… I think you might be letting your emotions get the better of you man
That said, obviously I’ve helped with troubleshooting a lot of cores over the years, and in the process that has developed through that experience, when someone’s core is going screwey and we’re talking about uploading hex files, the first thing I do is make sure that they’re using mios studio, and in the correct manner. I tend to try to avoid getting even to that stage, by recommending the safest option in the first place.
That’s not only for the person to whom I am responding (esag’ in this case) but also with respect to any others who may read the thread in future. Even if you consider that esag is safe enough to try midi-ox, you never know who may read this post later on, and what their situation is. Obviously, different situations result in a different chance of failure. In your situation or mine, that chance is very low. In esag’s maybe a bit higher… in the mystery-man’s stuation…who knows… Maybe his core is emitting blue smoke, and he will try MIDI-Ox instead, and make it worse I’m being silly, but the point is, it’s best to play it safe.
As for esag’s situation in particular, to be honest, “1%” is just a figurative number to say “not many” but it’s probably more like 10+ in reality. Given that esag is already having some difficulty, he’s also in another danger-zone that’s more like 80% attrition. I don’t think it’s really a good idea, in this case.
But my opinion should not dictate your actions, or your willingness to respond. If you’ve got an opinion, voice it! If everyone in the world kept their opinion to themselves when ever there was disagreement, we’d never talk at all - and nobody would learn squat, and this forum would be about banging rocks with sticks to make noise. Seriously man, all respectful input is good input I reckon, and you’ve always been respectful. Even though I have voiced a disagreement with you, I hope you feel I’ve shown you respect, as I try to do so equally for everyone.
Oops another post. *phew*
esag: try not to confuse MIOS (The MIDIbox Operating System which runs on the PIC chip in the Core module) with MIOS Studio (the java application that runs on the PC). MIOS Studio is specifically designed to talk to a midibox and perform midibox-specific functions like hex uploads and debugging, which is why you haven’t heard about it elsewhere.
I’ll explain what the two do a little, hope it helps. At the least, it should give you some good search keywords.
The OS:
MIOS. You shouldn’t need to worry about it. It’s equivalent to windows on your PC, it functions as a platform to run your applications. It will pretty much just sit there and behave itself, if you treat it right 
The app:
The app starts off as C code, which is compiled to generate ASM code (sometimes TK just starts there). The ASM code is assembled, and that generates a .hex file. That’s the final midibox application. Same deal as an .exe file on your PC basically. But like a PC, you have to copy the app onto the PC to run it…
The upload:
Normally, you have to use a hardware programmer to ‘burn’ a hex file onto the PIC chip. The MIOS BSL (bootloader or bootstrap loader) which is already installed if you buy from smash or mike, accepts sysex data to upload code over MIDI. Think of it like copying an exe file from one PC to another over a convenient interface, say, ethernet cable.
While it does this, it also sends some messages from the core’s midi output, to allow you to monitor what it is doing, and if it’s successful. I’ll come back to that.
The procedure:
MIDI-Ox:
With MIDI-Ox you can send a .syx file with the required sysex data. Sysex file handling is a generic kind of utility for midi, as you seem to have gathered. There are many apps that could do this job, but MIDI-Ox is very popular. In order to obtain the .syx file, you have to use a utility to convert the application .hex file (see ‘The app:’ above) to syx. There is a Perl script which does this. Then, you just send the file to the midibox, when it requests a code upload on startup.
MIOS Studio:
MS basically does the same thing as the above, but in the one app. You open the hex file in MIOS Studio, and it converts it to sysex data (like the perl script would) and sends it to the midibox. The big differences are ‘wait for upload request’, ‘smart mode’, and the awareness of the core’s protocol for reporting it’s progress (see ‘The upload:’ above).
These three features respectively provide: the restriction to send the file at the correct time, the restriction to only upload when the core says it is safe, and reporting of any errors in a human-readable manner. These are very handy to have, but they are not required for a successful upload. MIOS is very flexible, so as I mentioned above, any sysex sending app could do it. Naturally, the custom-built app for this purpose, has some bells and whistles.