Very long thread, so maybe I missed something, but why the cascading midi?
The SY-1000 and Gr55 both carry MIDI on their USB out ports. It’s not clear to me why you want a midi cable at all anywhere in your system. It only invites the kind of problems you are having. Why not connect all three to your PC by USB?
Here’s a long description of why:
A set of MIDI devices in series is nothing like a set of audio devices in series. With audio the device just adds its waveform onto the incoming waveform. Whether it’s processing analog or digital, it’s a trivial operation.
Not so with MIDI. It is a protocol, and you can’t just simply slap one stream over another and expect it to work. A typical MIDI message is a sequence of three bytes. If a device is trying to merge its own data stream with another device’s data stream it has to track the messages and know when the other device is done before inserting any messages of its own. If it’s sending its own data it has to buffer the incoming data, keep track of it, then send it out when it’s done with its own.
Adding to the complexity, MIDI has a thing called “running status”, where the initial bytes of a message are not repeated if they are the same as the prior message. When devices send a series of Note On messages, for example, they may send the first byte once (the Note On) and then the second two bytes for each additional note (note number, note velocity) without repeating the initial Note On byte.
When chaining devices, the second device may (correctly) see a break in the sequence, then insert its own message. When the next note message comes from the first device using running status the second device has to remember “I just interrupted the running status, so I have to add a Note On byte to the data stream or the next device won’t understand”.
Now add to that the fact that there are two different ways to send a Note Off message. You can send it with hex code 0x80 (a real “note off”) or you can send it as a Note On (0x90) with a velocity of zero. There have been longstanding issues with MIDI devices not correctly tracking, processing, or passing these “note off as a note on” messages. The primary reason for creating this second flavor of “note off” message was to not have to interrupt the running status. Unfortunately, many devices over the years haven’t handled these “running status note off” messages correctly.
For an even moderately decent programmer none of this is difficult to handle. Except to do it correctly the programmer needs to understand the MIDI protocol, and account for the fact that this stuff is often processed alongside the real time audio processing in devices like this. So sometimes you finish your calculations and add something to the buffer after the buffer has already been processed. So you calculated it all correctly, but it doesn’t go out and it’s hard to figure out why. (Been there, done that.)
So really short point: don’t do serial MIDI unless you have to. These kinds of devices really aren’t designed for it. In your case I’d connect all three of your devices to your PC by USB and take your MIDI from that.