Whenever possible its best to print all separations at the same time and even reprint all separations if needed. This ensure the same environment conditions as they impact the film.
Separations need to be printed in the same orientation at all times. Inkjet’s can slightly distort images when they are rotated for output by as much as 1/16th of an inch.
All programs rotate output, Adobe Illustrator has an “auto rotate” option in its print window. Turn that “OFF”. Automatic features that think for you are not always best.
Even rotating images even when “nesting” (ganging up) on an inkjet is a big no no, especially if printing at a non squared resolution such as 1440×720. Registration will be off. Even with a squared resolution such as 720×720 the very nature of the inkjet head movement can lend itself to a certain degree of stretch if separations are rotated within a set even if printed to the same piece of film.
Something to look at:
Open the History window in AccuRIP and click the symbol to the left of the file name (plus or triangle symbol) it will show the exact dimensions sent to AccuRIP from you graphics program and that AccuRIP sent those dimensions to the printer. If they match your first file printed then the issue is the printer and how it is feeding the media. If they do not match then we have to look at changes to the file itself. AccuRIP does not set or alter dimensions, its a passthrough.
This can be an easily overlooked when reprinting a separation to match a previously printed set.