Problems using two programs

I have created two separate programs for my AT89C51ED2: bootloader (0x0000) and normal program (0x2000). I use an absolute memory addressed variable to distinguish between the two modes of operation so that interrupts either execute code in the bootloader or call the appropriate ISRs in the program code (above 0x2000). The following is an example of the code used for interrupts in program code, in order to eliminate the usual pushes, pops and reti done by the bootloader ISR.

/** Timer 1 ISR.
	*/
void interruptTimer1(void) interrupt 3
{
	#pragma asm
	lcall interruptTimer1Mirror
	ret
	#pragma endasm
}


/** Timer 1 interrupt working function. This routine is used for delays.
	*/
void interruptTimer1Mirror()
{
	timer1Interrupted = TRUE;
}

This seems to work fine most of the time, but it seems that some of the program variables are being corrupted (idata and xdata). Is this a problem with the linker/locater not knowing about the separate bootloader program/project? Is there a better way to handle the fact that the interrupts always result in a jump to the table at 0x0000(ie. in the bootloader)?