Hi.
That doesn't sound so good, haven't heard of those exact symptoms, so just guessing for trouble shooting.
Inkscape comes with different compilations of the pdf converter, that can also vary with the os system
-try if regressing to 0.48 would work, or find a pre 0.92.
As far as I could see it some lpe-s in 0.91 produce weird artifacts. Namely the sketch lpe generates nodes too far from the original path.
Maybe some of the problem is related to lpe-s. Powerstroke is a "new" feature, the old spiro path can also produce strange results.
Dynamic offsetting can clutter up some parts of the drawing as well.
Try saving as different pdf versions too.
Speaking of "glitches", make sure your inkscape is set to the default or higher accuracy at the svg output settings.
If the measures of your design are extreme, there are more artifacts appearing.
Extremely thin outlines -0,02 px etc.- may be rendered wrongly outside inkscape, and gradients that are transformed too small may produce black bending in 0.91's cairo renderer.
On the other side 0.48's pattern fills were bad.
Also, as the gradient issue is connected with "extreme" transformations, maybe try to remove any unnecessary transformations.
They are present if you resized page to content. To solve that you would need to copy/paste everything to a newly created layer, maybe even nudge nodes.
Dealing with pdf-s, transparency is a major issue.
Try with different variations of object opacity or fill with 0 alpha value -one of them doesn't show up when saved as pdf.
Masking doesn't transfer, use clipping instead where necessary.
Maybe the font is not constructed well -that case I'd try converting text to path manually before saving as pdf, to see if it goes well.
Filtering can produce different results at different zoom levels. If you made a custom one with the convolution filter primitive, that may produce an unexpected look.
All in all, make the file as "dumb" as possible, and then by "divide and conquer" sort out which part of the file is not working.
If stuck on one part, share the file, maybe we can find the problem.
Other option is diging up the
bug tracker for related material.