i thought a dng (raw) file should be a direct result of the first process of the scan, which is in this case, a negative image (if you scan negative film). Have you check RAW option and save it as tiff, maybe that will make different result (i am not in front of any pc, i can only try to remember it)
It happen to me from the first day i use vuescan 8, and now 9. So i always mirror the curve line in photoshop raw software and tweak the light in reversed way. Maybe there is a better way, but i can survive with this.
As for batch scan, i think there is two concept mismatch. Batch scan is to control which frame to be scanned. But the frame it seld need to be defined in the multiple crop option. Setting may have lost/reset from moving from vue v8 to v9. So i believe you should define new set of multiple crop setting to match your film holder, or from v8 version, try to save the setting as a file (there is a command in the menu). Then try to load it on v9.
keep it small & simple :
M2-T BP, IIIc-T BP ST, H-RF, RD1, BII C-Heliar,
T is Titanium !!