So there was another long thread on Fluke 87 repair featuring users Manul and Multiple Cheese Slices, you should find and read it. The way the power supply is set up, the battery negative is below Vss. I'm not sure how it all shakes out internally, but the fact that the indicated negative voltage was actually present on the terminals when you checked seems to indicate that somehow negative battery voltage is leaking back into the input somewhere. One thing to try would be to put the meter in the ACV position (battery installed) and then measure with another meter with the black lead going to the com jack and the other lead to terminals 3 and 4 (one at a time!) of the front switch--if that's feasible. If your negative voltage shows up there, then you have a better idea where it might be coming from.