Are you still using the circuit that produces a short pulse at each zero crossing or did you change to the circuit that toggles the output for each zero crossing? I suspect you are bumping up against the MPGuino detecting ability.
The table on the wiki page has settings of 4000 to 16000 for pulse/mile on various cars. Yours being more then twice what anyone else has shown to work with any other car puts you in uncharted territory. I would divide your signal down to a frequency the MPGuino is known to work with.
I would use a dual flip flop to divide your pulse stream by 4. There are a wide range of options for doing this. Each flip flop can be used as a two to one divider and when they are cascaded you get a four to one divider. I would use a 74AHCT74 so you can take care of signal level matching and frequency reduction with the same part. The preset and clear lines get tied high and the following couple links show you how to connect the inputs and outputs to create various dividers.
Frequency Division using Flip-flops
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I think your just a fifty cent logic chip away from success.
Mike