Perhaps an issue with PB3, PB4, PA15

[mstrens]

In order to use those pins, the code has to ask a remap of pin and to activate a clock (RCC_APB2Periph_AFIO).

Therefore in main.c you currently have
RCC_APB2PeriphClockCmd(RCC_APB2Periph_USART1 | RCC_APB2Periph_GPIOA | RCC_APB2Periph_AFIO, ENABLE);

Still this line is active only if you are using UART1 instead of USB.
Quite similar line of code exist for "limits" and "controls" files but not in stepper.c
So I expect (but not tested it), that it will not be possible to use those pins for step, dir or enable stepper when USB is used instead of uart1.
It would be better to add a line in main.c in order to ALWAYS activate RCC_APB2Periph_AFIO

[Alfrederson]

They're currently used for flood and mist control. I can confirm they do not work with the current code because those pins are used for JTAG debugging