Hello,
I cannot find any direct relation between JoomSEF and pathway. If you are developing a site and you are adding a link to the pathway, to make sure they will go through the SEO processm you always need to use the sefRelToAbs function.
As regards the problem that SEO causing that the pathway is not shown (have not experienced that yet or does not work? -- maybe you could specify closer what does not work and what is the actual behaviour) some source code checks at the related site would be probably needed. But without more detailed specs of the problem we cannot help much.
Anyway, if you would like our admins to check the problem for you, you can purchase the support time at
http://www.artio.cz/en/downloadable-software/support-services.
Best regards,
ARTIO Support Team