Disclaimer: I'm no expert, and have no experience with that equipment.
I'm thinking it's a polyphony issue, as you originally suspected. If I've read your post correctly, you're outputting the MIDI file to your old Akai S3000XL, right? It has a rather small polyphony of 32 notes, which works out to an average of 2 simultaneous notes per channel, assuming you're actively using all 16 channels. I'm guessing that when you produced the dance tracks 20ish years ago, you recorded the tracks separately and mixed them together, such that the Akai S3000XL didn't actually need to play more than 32 notes at a time for any given track.
On the other, the MIDI soft synth(s) or whatever that Aria Maestosa and MidiYodi are using probably have a maximum polyphony of 128 notes, or something like that. What you might want to do, just to confirm or deny that it's a polyphony issue, is go into the settings for the MIDI soft synth(s) and change the maximum polyphony to 32 notes, to match the Akai S3000XL's polyphony, and see what happens.