It just occurred to me...the Transient Shaper has a fair amount of lookahead because, of course, it has to look ahead to know when transients are coming. I wonder if hitting PDC (or toggling it), or increasing latency, would help.
 
The way I get around dealing with plug-ins that have look-ahead is to render the the track, save the plug-in preset with the project name so it's easy to find, and then remove the plug-in. 99 times out of 100 I don't need to go back and use a different plug-in setting, but if I do, I have the preset available as a point of departure.