About R-44 markers:-
They seem to be somewhat non-standard when it comes to viewing them in DAW software. They way they work seems to be that every R-44 file contains markers 0 to 99, all at zero time, or possibly at some negative times. When you press the "mark" button, the first mark is given a real time. However, Adobe Audition doesn't see them as normal wave file cues (well, it does, but in rather garbled fashion). However, Wavosaur (tiny free audio editor) does see them.
Meanwhile, the next version of Reaper ($50 very fully featured DAW) can show cues in wave files, and optionally create timeline markers from those cues.
I've found that if I open an R-44 file in Wavosaur, then create new markers alongside the original ones (the work of a moment, and you can place them better than you did at the concert on the fly) and save, Reaper's next version will then see them. You only need to see them in one file from a multitrack set of course. And you can get them into Reaper's timeline by shortening the left edge of the file by a tiny amount, so the stack of unused ones doesn't show, then use the command to copy the rest onto the timeline.
Saves having to hunt through a long concert working out where each song started.
Alternative strategy, if you have pre-recording enabled, is to press stop in applause between songs, and immediately press record. That will create a new set of files with only a few milliseconds of lost material, as the pre-record buffer starts filling as soon as you pressed stop. So in your DAW you see each song as a separate set of files. But check at home whether yours is as gapless as mine when used that way.
Meanwhile I've emailed Edirol about the flakiness of their markers and I believe they are looking into it. Let's hope for a firmware upgrade to fix this issue in due course.