If I remember correctly, AkelPad was one of the apps that checks if its settings file (.ini) is read-only or not, and only complains if it's not read-only but it failed to write to it. For example, if the file isn't marked read-only, but is placed on read-only fs or made immutable, it will complain.
Hmm, in that case you could manually set the file as read-only using Wine explorer?
But also it means that Windows applications won't be able to "unset" the unix `read` permission (by marking it as read-only), which is something I'm more concerned about.
I assume you meant to say "'unset' the unix write permission"? My point above is that I'm not sure this is actually a desirable feature, i.e. at least in my experience it gets in the way more often than not, and I have a hard time imagining a circumstance in which it's a good idea.