Bad clock pulse on I2C EEPROM read
"What could be causing this malformed clock pulse? Has anyone seen this before?"

When I've seen this problem it's been because I didn't code my I2C driver correctly. It's usually something along the lines of incorrectly setting the I/O pin to an input for a few clock cycles while nothing else on the I2C bus is driving it. This causes the pullup resistor to start to drive the line high before the somebody reasserts the data line.