Sorry, I should give more details here.
As said in the faq Tony pointed me at, I deleted all preferred visuals from Emplode, without any editing of the config.ini directly. Re-synchronized and everything was working again. Also, by going back to the config.ini, all the lines in the favourites visuals sections had been properly deleted.

So, it seems that for some reason the config.ini fills up of those lines when some visual is selected as favourite in emplode, and this prevents it from being properly handeled by hijack. Or is my guess wrong? Anyway the question remains (unless I did not look properly at the faqs): why are all those lines being created in the first place? Sorry if this has been discussed already in the bugs section of the bbs, I haven't looked at it yet, so feel free to disregard my question in that case.

Thank you Tony and Mark again fro your help.