Handling jobs with lots of transparencies can cause problems (e.g. in speed).
Ripping these kind of jobs can be very slow because the transparencies need to be resolved during ripping.
Since version 12.1 (part of Suite 12 Assembly 3) we offer faster output for jobs containing lots of transparency. A lot of such jobs can be speed up by partially resolving up-front (during pre-ripping).
There is now a new Resolve Transparency option in the Pre-Rip tab of the Expose and Proof tickets.