I don't have either of those instruments and there are others here with more expertise that may be along soon, but i have just a few quick thoughts.
1) Measuring resistance at 100M and above is always tricky. You need ceiling fans and circulation off, doors closed and you may need to stand back from the bench to get the readings to settle.
2) Most test cables won't work very well. I would try taking two solid conductors out of a phone or LAN cable, connecting them to Pomona MDP-style connectors and then twisting them fairly tightly. Alternatively, use Pomona 1269 BNC-to-banana and use a BNC-terminated coax cable. Or simply use the twisted solid conductors directly to the binding posts if possible.
3) Guards are tricky. Some are passive, some are driven and they can cause problems if used incorrectly. Unless you study your manual and understand what the guard actually does in each instance, or you have definitive guidance as to how they should be connected, I would try omitting them entirely for now.
4) Look at the specs for each instrument and figure out what the actual uncertainty is at your measurement point. The 'noise' may be a significant part of the uncertainty--so if your total uncertainty budget is 5000 counts, don't be surprised to see 2000 counts of noise. Don't skim the specs, read them carefully.