Pre-Empeg days and using Lame (3.87 at the time) I had the same problem; fine on PC but sudden bursts of squeak noises seemingly random on my CD recorder with MP3 play-back capability. Only thing was, noise wasn't random, I could go back to the same location of the track and it would be there in the same way. Note there weren't problems at either beginning or ending of tracks.

Digging a bit, I found out that adding "strictly enforce ISO" to the Lame command line solved the problem, I haven't had any problems since with any MP3 hardware-decoder equipped stuff, nor with my Empeg, for that matter, but I haven't tried without so it may well not be an issue in that particular instance.

http://www.r3mix.net is a very informative site.