Thanks Leviathan and kode54,
I did understand what was going on, drawing obvious conclusions from the first article of this thread. I also know about Musepack being gapless. But I didn't know how cue files are played track by track.
I just wanted to illustrate a side effect of the slow seeking.
Just a thought, how about using something like the old seek table hack, but start decoding roughly 2 or 3 seconds before where you should start playing, instead of from the beginning. This might solve the occasional "minor" problem.
I personally prefer the old behaviour because, when I don't seek it's not an issue and when I do I'd rather choose 1 second lack of bass over 1 second waiting for sound. (1 sec. is just an example here

)