thanks, will think about it when this continues.

Maybe too early to party but I've changed
Set page base href value: only base to full seo

now and since yesterday theres no new wrong link popping up or any other visible sideeffect.

sorry to bring this back but it's still happening. But we were able to find the source, its only happening when you edit an article (backend at least). Once you save the links come up. Not every time but it only affects edited articles (we use latest JCE-editor). Haven't noticed before cause we have several active writers. Thats even explains why we never see an issue with auto-generated domains in backend.

And another issue we found:
Joomsef is not able to switch by given domains anymore. With JS3 (&Joomfish @J1.5) we used
domain.com/english.html and domain.de/english.html (cause translating urls was broken sometimes in the past...)

with he new one we like to use translated urls (cause even disabling that option does not work, it still translates) but it's not able to determine that
content on .de has to be german. Instead
domain.de/english.html redirects to domain.com/english.html instead of domain.de/german.html
the setting is set to 'redirect to correct domain'
it only works if the category is translated too.

furthermore paginations are broken. Had to disable this cause sometimes page 1 got page 3, page 1 got left out, page 2 is actually page 3 aso. Fully unreliable.

Language Switcher is often given completely wrong links. Even if all links are correct in backend it sometimes fetches another link from the same component as translation.

I'm sorry I don't know how to help you with the original problem, I can only offer you our paid support to check it directly on your server.

Disabling translation should work for articles, but we'll check that. The redirection is working as expected - the domain is redirected according to SEF URL, not the other way around ("redirect to correct domain").

Please post some examples of the wrong pagination links together with their corresponding non-SEF URLs from JoomSEF's URLs Manager, thank you.

For the language switcher problem, please try disabling SEF completely in Joomla's Global Configuration and check what non-SEF URL is displayed in the language switcher and whether it corresponds to the correct SEF URL in JoomSEF's URLs Manager. Also make sure that you have cleared JoomSEF's cache.

thanks, will send you a mail in a few minutes with necessary data.