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That special font on the bottom of checks is (was) known as "micro-encoding" IIRC and it isn't only a special font, it uses a special magnetic ink, to make it machine readable (from the days long before computer OCR was even a dream.)
Again, IIRC, in the part of the sorting machines which read those codes and sort the checks, other inks are "invisible", so that a 'loopy L" for example, shouldn't have interfered with the sorting of the check.
Some sort of human error is more likely -
It probably won't happen again, but keep your eyes open - it might be some sort of elaborate scam which could hit you again.
Late Update: Hrrmmm, TPM Reader SW agrees ...
In a previous life, I used to work at a bank, as a humble teller, to help pay my way through college, and I can tell you that the signature on a check cannot cause a check to be paid from the wrong account.
That line of numbers (and lines) at the bottom of the check, representing the account number and bank routing number are encoded with magnetic ink, allowing the information to be read by machines. The ink, from the pen with which the check would have been signed is not, and, unless banks have completely switched over to optical scanning, it could not cause the account number to be misread, as it would be effectively invisible to the machines. Trrust me, I have handled thousands upon thousands of checks, and you wouldn’t believe the condition in which many of them are presented. If a mere swoop of a pen could cause this sort of problem, it would be happening on a VERY regular basis.