Update to this:
Found that closing CCS, then cleaning the project and reprogramming fixes the skipping issue. I added in the code which worked on the mpu6050, works as it used to. I figure my 16-bit addressing code is incorrect in its use of the I2CMasterControl function somehow, though I find it odd how I can access 0x0000 and 0x0001, but no other address. That seems weird. Also seems weird that I2CMasterDataPut is linked to I2CMasterControl and I cant manipulate the MDR register out of a sequence?