Problem signing PDF with certificate

Sometimes when I'm signing document with a certificate I have a problem that after saving the document there is no signature in the file. 

There is no error or anything. Everything look normal except missing the signature in PDF file.

Nothing seems to help, I've tried reinstalling certificate, reinstalling Adobe Reader, it doesn't help.

After few hours or sometimes on the next day I can normally sign the documents.

Does anyone had similar problem?