This really does look like an OS issue.
Forgive me but I do not understand the significance of case-sensitivity of sattelite resources. Perhaps the obvious question is- how does your system work, without smartassembly? (How do you get the file system to respect case-sensitivity such that no over-writing occurs). Could it be that seperate smartassembly projects are needed?
You can embed protected assemblies as well as merge- this may be how you can best workaround this.
>>Also; is there some form of bug tracker, or similar where I should be reporting bugs?
Not publically available, sorry, no. This forum works and, if necessary, we open a formal support ticket if you write to: firstname.lastname@example.org