RIPs sometimes print the page slug info based on the the page number of the "job" and not the page number of the document. Thus if you print, say, a 200 page magazine all at once then the slugs will have page numbers 1 through 200 on them, making it easy to see the page order even though some pages, ads for example, have no page number at all.
If you then go back and re-print just page 5 the slug will -- with some RIPs and some software -- indicate that the output is page 1, regardless of what the software thinks the page is. Now fitting it back into the right place becomes a hassle.
I have no idea if InDesign can overcome this, but I do know that in the past I've put a "true page number" text box outside the margins (that matches the document's page number) to print as part of the bleed, a number I can use to slip pages back in the right place when they're individually output (or more commonly, output in batches, say a register at a time).
I assume that's what kamcl is talking about.