Sorry, but my workaround doesn't involve using the computer to capture the entire arranger output. Far too much data nowadays, especially with lots of sys-ex running down the pipe, which interrupts clock signals' timing. I can't get my G70 to do this either, whereas my G1000 had no trouble. I guess things are just getting too complicated. But try filtering sys-ex from the Korg's output... this MIGHT tighten up clock lock

but it might cause some things to get recorded not quite the same as the original sound. Worth a try, perhaps. How is USB for MIDI between the two? Any better?
Basically, If I have to redo a section, I simply use the Arranger Recorder (the one that 'captures' the entire machine) to record JUST that section, then save it as a new SMF in the arranger, which I can (after transfer) open INSIDE the arrangement that has the earlier capture on it in Cubase. I can then chop out the 'bad' section, and drag and drop (or insert) the new section into it, then save as a new SMF.
I would have thought Sonor7 should have been capable of such a simple task... Try opening an SMF in Sonor, then ask it to 'Import' another one. Maybe you can get it to open in the same arrangement, or maybe it opens a new, parallel one, in which case you ought to be able to copy and paste between the two. I'm afraid I know next to nothing about Sonor (I'm a Mac guy), but this seems basic in any modern computer sequencer, even if it gives fits to the on board pieces of junk!
Give it a try...