I can duplicate your problems. I erased the paint and repainted everything, and nothing changed.
I printed it to PDF from both Softplan's EXPORT TO PDF and CUTEPDF WRITER. Softplan's output was much cleaner. Not sure why that would be.
I did notice that the discrepancies change at different zoom scales. I would have hoped that 100% would be perfect, but no ... but it is possible that it's in the writer design. Maybe try a few different PDF writers (there are literally hundreds of free ones available) and see which you think gives the best results.
In each of the attached PDF's, the top one is yours, and the bottom one I repainted.
The TEMP file is Softplan's EXPORT TO PDF, the TEMP2 file is CUTEPDF WRITER.