To long for a comment:
you can find other questions on this side reporting problems you have, for example this question and have a look to the answer I linked to.
After running your given MWE
mwe.tex with current MiKTeX I get the two files
As you can see the second entry is missing in the second file. Therefore you can not see the added pdfcomment.
As you can read in the linked answer above the culprit is package
soulpos, which shows the following version number in my log file:
soulpos.sty 2012/02/25 v1.1 Fancy underlining.
It seems the bug is not solved in package
Please make a bug report to the author of
My used TeX distribution is
pdfTeX, Version 3.14159265-2.6-1.40.20 (MiKTeX 2.9.6960 64-bit).
To answer your last comment "Are there other ways to get the same effect which can be used also in page header/footer?": As far as I know there is no other way for the same effect. The culprit is here, that this effects a heavy viewer dependent, some viewer shows it, most of them not. And the problem is that you can not know which pdf viewer a reader of your pdf is using. I do not think it is worth the time you have to invest to get that solved ... Sorry for bad news ;-)