I think it may be getting stuck the second time around at the serial part.

Could give this a try...
Code:
'-----[ Get RS232 Data input, and assign into MSB & LSB Data to be displayed ]------------------------------------
GetSerial:
SerIn RS232,T9600,RS_Data	'Read Serial Data on Pin RS232 (A.4) and assign value into "RS_Data"
GetData:	
					'Assign any of the "0123456789-" characters to "digits".  
	LookDown RS_Data,["0123456789-"],Digits	
					'Match number from RS_Data, and assign 7seg data to it into Digits.

	IF Counter	= 0 Then										
	LookUp Digits,[$3F,$06,$5B,$4F,$66,$6D,$7D,$07,$7F,$6F,$00],MSB	'If "Counter" is "0" then store in MSB.
	Else		'(	0	1	2	3	4	5	6	7	8	9	- )
	LookUp Digits,[$3F,$06,$5B,$4F,$66,$6D,$7D,$07,$7F,$6F,$00],LSB	'If "Counter" is "1" then store in LSB.
	EndIF


	IF Counter	= 0 Then	'If counter=0, then this is the first digit to be processed.
	Counter		= 1 		'Now make counter=1, to show (next time) that the 2nd digit will be processed.
	GoTo GetData			'Repeat to get 2nd digit to process.
	Else 				'
	Counter		= 0		'Otherwise, make counter=0, ready to process 1st digit of the next "2 numbers to arrive".
	EndIF				'		
			
	Return				'Return back to Start, and display MSB & LSB onto the 2x 7-Seg displays.


'-----[ Display MSB & LSB Data onto 2x 7-Segment Displays ]-------------------------------------------------------

Start:

	'UNITS:
	seg7 = LSB		'place data "LSB" onto PortB 7Seg info.
	units_com = 1		'ENable UNITs cathode.
	Pause 10		'Keep UNITs ON for 10mS before going back to TENS
	units_com = 0		'DISable UNITs cathode.

	'TENS:
	seg7 = MSB		'place data "MSB" onto PortB 7Seg info.
	tens_com = 1		'ENable TENs cathode.
	Pause 10		'Keep TENs ON for 10mS before going back to UNITS
	tens_com = 0		'DISable TENs cathode.

	GoSub GetSerial		'Go and check for new serial numbers arriving.
	GoTo Start		'Repeat this section again, dispaying the 7-Seg data etc.


'-----[ END ]-----------------