It looks like you have some extra capacitance on the bus.  There should 
not be any capacitors bridging the I2C data and clock lines. Some of the 
third-party universal interface cards have extra capacitance, so take those 
off.

I have never heard of an I2C part with built in pull-up resistors.

Do to the multi-drop nature of the I2C bus, pull up resistors are almost 
always external. There are some "weak pull up" resistors you could turn on 
in the BBB, but are too high in value for most applications.

I suggest you read up on how to select pull up resistors for an I2C bus.  
Phillips (now NXP) initially developed the bus and has good documentation.
Google: NXP I2C bus documentation

But the short answer is that for a 3.3V bus, resistors in the range of 1.2K 
to 3.3K should work fine. The value is not critical. You want to pull 1 to 
3 mA through the resistor when the bus is low.

--- Graham

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