Wish I could help... Sounds like it's my own setting somewhere in the imagesetter that keeps my Quark from defining LPI.
I can tell you, though, that I've had other weird, random problems printing to other devices in my shop from Quark 6. And, like you, if I open the same file in Quark 5, they print the way they should. One example is, I have to go to Page Setup last and pick the printer and page size in order to print multiple copies of a doc. If I don't do Page Setup as the very last step, it only prints 1 copy. Another problem is colored text typeset in Quark prints in different shades. If we have 8 up, for instance, the same letters in the same position in all 8 ups will print incorrectly, but it's not necessarily all occurrences of a particular character. But if I save the file down and open in v5, it prints correctly. I have some people researching it, but no luck yet.
So, long story short, I think Quark 6 in OSX just has some odd problems with printing. Maybe Panther would take care of it? Maybe not... I don't really want to spend the money on it to find out it doesn't help. Hopefully Quark will put out a patch. Again, wish I could help solve your problem, but it unfortunately may be that there is no solution right now. Argh.