Huh, not sure how much of that is due to your printer versus how the document is formatted; I've not noticed that stripey pattern before, but I'm guessing that's specific to the color laser printer or whatever it is you have, moreso than the document?
Is interesting that, it seems like the DPI itself is varying between formats. Maybe the print dialog is set differently too? (See any "draft" or DPI/resolution settings in there?) Maybe the printer "knows" and just doesn't bother for the one?
Have noticed sometimes my printer gives low resolution on later pages, I think because the spooler accidentally runs out of buffer size or something. That's probably specific to my computer or printer though, and it's not consistent (i.e., I print off say 10 pages and the last few are blurry, I re-print the last pages individually and they're fine; like I said, spooler memory or something).
I don't know how Altium formats documents those ways (load it up on a PDF object editor to find out?), but yeah they are different, it's a different method than Smart PDF/Output Job. The latter is richer and more consistent/portable (portable in the sense of copying the OutJob to other projects and so on; well, in some things like SCH outputs, but not others like PCB layers you need to customize for whatever layers the PCB uses, if different), so I would recommend using it.
Tim