Hi,
I use T89C51CC01 for a long time. No problem with UART and its clocks.
Yes you are right - bootloader works at 57600 (you know, here it works at 115200 with osc 18.432Mhz :)
It is because bootloader uses T2 itself. Now about "START APPLICATION" from Flip. The problem of current bootloaded version is that it does not disable T2. When user pushes the button and FLIP sends "start application" command the following code is executed internaly by bootloader:

	mov	A,hex_buffer+1
	jz	hex_hardware_reset
	mov 	DPH,hex_buffer+2
	mov	DPL,hex_buffer+3
        clr     A
	jmp	@A + DPTR

hex_hardware_reset:
	mov	WDTRST,#01Eh
	mov	WDTRST,#0E1h
hex_wait_reset:
        ajmp    hex_wait_reset

Hmm, as for me so I do not see any problem: there are at least two solutions:
- start application with Reset (checkmark in FLIP);
- stop and re-initialize both timer2 and UART before utilize it (as it is indicated in Bootloader Errata datasheet).

Good days!