This is a known problem with multi slots, let me explain.
It happens only wirh a few games, the one that have 1MB P1 + 1MB P2 (or 2MB single P rom). The problem is that neosd will enable banking on the 2nd MB area but those games don't have banking hw so they never reset the banking when selected. This should not be an issue, but on multislot, when a banked game is selected, neosd will see the bank switch writes even if it's not the selected slot and so, when selecting the game, it has an invalid bank and never sets the proper one.
Neosd pro firmware has this isue corrected, but I haven't backported it to normal neosd yet.
Also the issue depends on the game next to the neosd. If it's a well behaved banked game, that leaves bank 0 set before calling into bios, it will work. Kof99 and garou are especially bad behaved
Which games do you have installed in your mvs (order is important)? Maybe it can be worked around by setting them in a different order.