In a previous post we narrowed it down to the fact that older versions of mIRC were in some situations storing the [logging] section without the full path information. The new mIRC fixes this problem, however it can't correct the incorrect paths in your old [logging] section.

If you turn off logging for those channels and then turn it on again, the [logging] section should be updated with the correct path and should be logging to the correct folder from then on.