AntF,
The fact that a PDF works while other software from Adobe does not is curious because Adobe invented the Page Description called Postscript. It was the language that allowed laser printers to get rid of pixelated rough edges created by dot matrix printers. Does Illustrator have a problem printing the components before they are placed in InDesign? If the job is too large to spool to the printer or the printer has too small of a buffer to take all of the print command at one time, you will have a break in instructions that might result in incomplete pages.
Because Adobe created the PDF from its Postscript language, it is completing the printer page layout instructions all at once. The printer sees a complete set of print instructions as a document and not as fragmented instructions from the application that created the document. Some programs used to say 'printing page five.' The application was sending each page one at a time. PDF converts to printer commands before sending them to the printer.
Mechanically, once you get a signal to the printer, the problem is rarely software related. If in doubt, disable all print spooler or print monitor software and print directly from the application to the printer. That includes disabling 'Drag and Drop' printing.
Here is what happens mechanically inside the printer. The paper feed roller picks up the first page. An electical relay signals the rubber roller to pick up the first page. The roller is designed to mechanically rotate into position and then back out. The roller then needs to stay out of the way until it is needed again.
There is a second relay that also affects paper handling. The printer has to delay the second page until the first page is out of the way. Some actions are mechanical, some are electrical.
On our Laserwriter IIG, the page separation relay would stick just long enough to add an extra one inch to the top margin of the second page. The official fix was to clean the contacts to remove gum from the metal plates. The sticky contacts slowed down the timing just long enough to throw off the timing for the toner drop but not enough to cause a paper jam.
Your printer may be experiencing enough of a timing delay to cause a paper jam. A good cleaning or servicing would be good. Go to
http://www.fixyourownprinter.com
to find resources.
A search for the Laserwriter 360 shows 241 discussions on that model.
I do not have the schematic on the 360 but we could certainly take one apart to answer a specific mechanical question.
Jim~