Two bulb fixture with 2 ballasts
I'm a bit alarmed when I hear you say "capped off my yellow wires".  A few ballasts do give that instruction, but not for 2-bulb use.  I fear you might be matching up wire colors and not following the schematic on the ballast.   Thing is, if the old ballast was instant-start, that will totally backfire. As you can see in these typical schematics, red and blue do quite different things on the two types of ballast.  (ignore the LED one).   



These schematics are not universal, only common.  Yours is on the label on the ballast. 

When converting instant-start to rapid-start, the other issue is shorting .  The instant-starts only connect 1 wire to each end of the bulb, but it goes to both pins.  This is almost always accomplished with a shorting lampholder (tombstone), which accepts one wire and connects it to both pins.  

A shorting lampholder will have 2 holes for wires, but that's for daisy-chaining (as in the red wire above), not for 2 separate wires.  A non-shorting lampholder intended for rapid-start ballasts will have 4 wire holes, 2 for each pin.  The extras are for daisy-chaining, as in the yellow below.

Unless there's a visible wire to remove, there is no way to turn a shorting lampholder into a non-shorting one. You just need to buy replacements.  They are fairly standardized, and I buy mine online for about 60 cents a tombstone.  I buy only non-shorting types, it's easy enough to convert one into shorting with a wire.