What app is it, is it a 16bit program?
Also, what exactly does system function call mean? Is it one affected function or multiple?
Does it work reliably on windows?
IMHO it wouldn't hurt to open a bug report, be it just for others who have the same issue. You could try to come up with a patch, either as workaround or possibly as upstream-able change.
Regards, Fabian Maurer