How important is it to layer objects on the page for printing?

Question

We are using InDesign CS3 on a Windows XP system and then sending to a RIP and then to an older Panther Pro 46 film printer.
We have lots of little problems, but one of the issues that happens occasionally, that we can't quite resolve is that for example...
When sending a job to the RIP 25 out of 26 pages will print fine (with all the separations and marks intact), but one of the pages, for some reason, is not properly printing the text or images (certain blocks of text print and certain ads or images drop out) and the marks are missing (registration, crop, color bars).
A friend told me that it is best practice to place images and text on separate layers. When we move objects onto different layers, sure enough, things start showing up. Unfortunately, this hasn't solved the problem completely. Sometimes, certain text would reappear while other things would disappear.
My guess is that we aren't moving the correct objects onto the right layers? Does it matter what goes on what layer? Does it matter which layer goes on top? Or is this all irrelevant?
Also, if anyone can point me to a good reference to press related resources. InDesign is new to us, especially on the PC, so I'm sure we could avoid many of our problems with some basic guidelines.
Thank you,
Joe

Answer 1

I also have an old RIP system although not exactly as yours. I have a page limitation (which is ironically 26). Anything over that page amount gave us issues that sound very similar to yours - Now, I just limit the number of pages per file. We prefer to flatten the files (now that we know the issue) as the rip will drop its own color space onto anything that has transparency. You may not have the color critical clients we do, but that is one reason why we flatten - and also that color is most appreciated when printed with its own attributes from a native file.