Welcome to pinside!
I’m sure others with more expertise will chime in, but my guess(!) is that bypassing the hold relay has something to do with this. During the normal startup routine (i.e., without the hold relay engaged already), I assume that power would get distributed through the transformer after other relays engage (w,e,etc,) and other parts of the routine are completed. I assume that the sb MB switch prevents the o relay from engaging until it should during a normal start up routine. Again, this is just my best guess based on my interpretation of the schematic and description of the issue, but it could be tested by reconfiguring the hold relay to work as it originally worked.
Best of luck!