I've "solved" it by going to Setup/URL Translator and setting up a system forwarding from "site2" (the folder that holds the objects for this site) to content/view/full/145 (the node that holds the homepage article). I repeat, the nodes are different, site2 being 141 and the homepage article being 145. IndexPage is set to 145, yet it keeps showing 141.
I'm glad it worked out, but if anybody can give me an explanation I'd appreciate it.
Besides, this workaround has the lovely effect of being active for the admin siteaccess too, and I can't go into the "site2" folder anymore, it redirects to the homepage article below. It makes adding new folders or articles rather tedious, having to move them around after creation.
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