The default template for Writer in LibreOffice 4.2.4.2 (I use it on Windows 7) has the Heading paragraph style defined with font size in pt. Both Heading 1 and Heading 2 (along with Heading 3 through Heading 10) are linked to the Heading paragraph style and both have a font size defined in percentage relative to Heading.
If you say you (manually) linked Heading 1/2 to Heading, it suggests they were not linked before. Linking does not automatically make styles inherit style elements like font size from their linked counterparts when an explicit value was already set (this is by design; it could mess up existing formatting).
So in this case, you should manually (re)define the font size of Heading 2 to be a percentage by entering the percentage value in the style properties - it will then use the linked style’s font size as the base size.