FYI, so others may perhaps avoid some inconvenience and time lost on this.
When un-checking "include suppressed components", it generally works as expected. However if there are components with some instances suppressed and some instances un-suppressed, those particular parts are not pack and go'd into the target folder. Those parts exist in the new assembly, but they refer back to the source folder, which is of course not what pack and go is all about. This includes suppressed patterns (like open/alternate positions, etc...)
For now, it seems best to avoid un-checking the box (for me anyway).
SPR 1050411 has been issued for this, no time-frame for fixing it is listed.