If you opt for the $123 XL version it's is a bit more to learn, but maybe not more difficult really. I know that may sound odd, but JJ OS's especially the XL one kind of are filled with all these additions or tweaks to the Akai OS that even beginner and intermediate user are often like, "yeah that makes more sense, or is less cumbersome". A lot of "why didn't Akai just do it that way in the first place?"
Over the years JJ has added so much to the XL version it's fair to say he's made the 1000 and 2500 double the machines they were under the Akai OS's. Both Akai OS's on those machines just got a few updates and that was it.
But as far as the free one it's generally the same as the Akai one. With more stability and the GPE I mentioned, which if it's free is certainly worth trying. (GPE is a lifesaver).
The comparison charts are here.
http://www7a.biglobe.ne.jp/~mpc1000/mpc2500/chart.htmScope out the first two columns and you'll see the exact differences between JJ Free and Akai 1.24. Again the screens themselves are not so different that your Akai manual can't be still used. You'll just notice little bits are slightly different, and just more logical.
I still have to flash the 1.24 OS over here and see what happens with a CD on that one. Not sure what time zone you're in but I'll have that done and post again tonight. Although it might be one of those things that isn't repeatable on another machine.
That the CD played right previewing it and while sampling it would seem the drive itself is OK. So if the gain was too high or some weirdness with the threshold setting (I just left it at default), I can't think why that happened when what you did was so basic. (rec/sample. preview, assign...)