Fixing the VBR headers with MP3TS should have done the trick for you.

Just for the heck of it, try running VBRFix (FAQ entry here) on one of the problem files and see if the empeg likes it (use Replace Tune on the rightclick menu to replace a tune in the player).

If VBRfix does the trick, then it might be a bug in Tag Studio.

Even then, if the "bad" file looks fine in WinAmp, then maybe there's something the empeg guys are missing in their VBR calculations. Empeg guys?