Sounds horrible! And it sounds as though you've tried all the obvious stuff.

I wonder if: You're saving to a server? Perhaps there are corrupted fonts or font caches? You're using Save As every so often? You're using any plug-ins that might be causing weirdness?

Obviously, most ID users don't have this issue. Not sure what could be “special” about your set up that would cause this.

I don't think there is any way to control the order of the seps. You could print one plate at a time (using the Output pane of the Print dialog box) and then create PDF files of each and then merge them into a single pdf (if you really need them as one pdf file).

Jongware: “you might want to allow more than 9 consecutively numbered headings”

David: Umm… no, at that point I would send the document back to the client along with a 3-day old dead fish (which usually ensures they don't call me back).

Biggedybong: You are right that there is much to learn. Jongware is a great help. Also check out: http:/indesignsecrets.com/grep for more resources, including books and videos on the subject.

I think this should do it:

^(d.)+

Probably just has to do with what percentage you're at. But for accuracy, hold down shift key while dragging a guide to snap it to the nearest tick mark in the ruler.

Create the color swatches in the swatches panel while no documents are open. This will add them to all future docs you make, but not to previous docs.

In this case I would just make a 2-page document: one page for each side of the sheet. The pages should be 6 x 4. No need for margins, probably. You can put a ruler guide down the middle to indicate (on screen) where the fold will be, or draw a tiny line in the middle that actually does print if you want that instead. I don't have a 4 x 6 printer, so I'm not sure how best to print to that.