I noted in the previous log that the failure to run at faster baud was probably clock related. Today I built a binary that dumps the oscillator and clock configs to see how the bootloader and reboot works, and here's what I found - "Letting the bootloader configure the clock" is bad. 

Here's the clock config from both:

  OscillatorConfig:
  OscillatorType:15 (all of them)
  HSEState:0
  LSEState:0
  HSIState:1
  HSICalibrationValue:16
  LSIState:0
  PLLConfig:
  PLL.PLLState:1
  PLL.PLLSource:0
  PLL.PLLM:16
  PLL.PLLN:192
  PLL.PLLP:2
  PLL.PLLQ:4
  Obtaining Clock Config:

  Obtained Clock Config

  ClockType:15
  SYSCLKSource:0
  AHBCLKDivider:0
  APB1CLKDivider:0
  APB2CLKDivider:0
  Flash Latency:5

So, that's what is wrong. If I attempt to initialize the oscillators, the board hangs, so I need to debug to this and figure it out.