First, we have changed the default value of that option from Yes to No for consistency with ndk-build. Therefore, the solution upgrader changes its value to Yes if it was not set explicitly (so as to keep the old default’s value for old projects).
Second, we have incorrectly included crtbegin.o and the like even if Ignore All Default Libraries was set to Yes. Now we don’t explicitly include these files in any case (again, to be consistent with ndk-build).
As a result of these two changes, we have unfortunately broken the building for some users, as in your case. Turning that option off is the right way to fix it.
UPD: On a brighter note, these changes have fixed some situations in which correct project building was not possible at all.