Hi!
I am very troubled about one thing which keeps on appearing all the time. It often happens after I import a figure (a svg file from Mathematica) into my figure. I use the import command, because the copy paste does weird things too... Anyway after I am finished and save the file as eps, in inkspace everything is visible, but in the eps many things hide suddenly (see the two images. Can anybody help me what I'm doing wrong? This problem occurs often when I add some labels (note the text "no I" in original disappeared too).

PS: I run Inkscape on Mac, Snow Leopard...

Hi and Welcome to the Inkscape forums!

Can you describe how you adjust the settings on the "Encapsulated Postscript" dialogue box?

i.e.,
__________________________________________
Restrict to PS level [PostScript level 3/PostScript level 2]
Convert texts to paths [ ]
EPS+LaTeX: Omit text in EPS, and create LaTeX file [ ]
Rasterize filter effects [ ]
Resolution for rasterization (dpi) [___]
Export area is drawing [ ]
Export area is page [ ]
Limit export to the object with ID [_____]
__________________________________________

My issue here is:

1. I have no idea what settings made this error;
2. I have no need for EPS files, so I am not an EPS guru.

I also hesitated to answer, because I'm not familiar with what you're doing, i.e. - Mathematica, Save as EPS, and on a Mac. By the looks of your results, it looks like some objects lack transparency, and are covering up other things. But it's hard to say....

In addition to the EPS dialog settings, it might also be helpful to know which parts of the image were imported from Mathem., and which parts you added with Inkscape. It it's too complicated to describe, even with screenshots, you could upload your SVG file as an attachment to a future reply. The those of us who are knowledgeable about these things (probably not me, lol) can download and examine the file.

Oh well here's one quick thing that might help (probably not, but won't be hard to try anyway). For some reason, if I'm having trouble with Save As 'some other non-SVG format', I've found that if I save it as an Inkscape SVG first, then Save As 'the other format', it somehow makes it work properly. I can't explain why, but it has sometimes helped

Could it be this issuehttp://www.inkscapeforum.com/viewtopic.php?f=5&t=9094? Although mine didn't happen with eps...

Or this: viewtopic.php?f=6&t=9585

I'm wondering about a few more things too, in particular:

1. is this problem consistent, or intermittent?
2. is the document's page resized to match the graphic before Save a copy (Ctrl+Shift+Alt+S) is selected?

With only screenshots available (what application do you use to view the EPS file?), I can only guess - but some of the details remind me of these reports:
Bug #645256 in Inkscape: “Incomplete picture when saving in eps”
Bug #694553 in Inkscape: “Save a copy...EPS fails when many paths”

Not much I can advise here - in my tests with the files that had been attached to the bug reports it only depends on the version of an external library (cairo), not on Inkscape's code itself. I'm not aware of workarounds - possibly you could test with Inkscape 0.47 (the Inkscape packages provided for Mac OS X do include the external library, and 0.47 uses the older version which did not reproduce these errors).