Try a different way of making PDF's. For instance : Pdfcreator.
You'll see that it makes a difference.
Even with other PDF solutions it still can have issues.
SW layers can perfectly deal with different colored layers as long as you use the same color for them all.
The worst thing i've ever seen was having different colors for different elements in PDF (even having different results between pdf's created in different manners), as well as being different in printed from DRW and having a different result when converted to DWG. None of them being the same as on screen. Or in other words, not being able to get it printed as it was viewable on screen.
Thanks Peter De Vlieger
Using PDFCreator would solve all the issues but would not allow me to use the feature of creating PDF documents automaticaly with PDM check-ins.
Wow, I feel guilty... saw this post while searching for the same issue, just thought it was a really old one, not todays :X
I'm also having the same problem, but for eDrawings as well (which we use almost exclusively, for checks and approvals and whatnot). There isn't another way to save as an eDrawing that would work, is there?
I've been in contact with ntcadcam support who say the problem occures in 2012 SP3.0 that I am using SP5.0 and 2013. It is a problem with the blocks and only using programs like PDFCreator that print to PDF will it work. They have forwarded to solidworks..
We will see what happens maybe thy will release a patch for it in the next SP for 2013.
Perhaps by now it got high enough on the priority list to them taking care of it. We can hope.
When we had that one really bad issue it did also have a different result (different then all the other results) in edrawings as well.
There's only two things left that one can do:
1. start all over making the drawing and hope for the best
2. suck it up and try to get something halfway presentable out of the mess