18F4431 PWM question

I am using a function generator for the input on this board. Based on the PWM, the 4431 will change its PWM channels too. The input signal is 100 hz. There is a 'pause' in the output side on PWM1,3,5,7. I am assuming I have something set up wrong and its not a hardware problem. I have tried this on four 4431's. The PWM will be fine then go high for an amount of time then go back to pulsing. If I am at 50% duty cycle the pause is the smallest. 20 and 80% is the worst. My function generator won't go lower or higher.

Code:

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define CODE_SIZE 32
define osc 20
Include "modedefs.bas"        ' Mode definitions for Serout
Include "Elapsed-18.bas"
OnOff1        var    PortE.1            'Input Signal from GPS to activate/deactivate row
OnOff2        var    PortE.0            'Input Signal from GPS to activate/deactivate row 
OnOff3        var    PortA.5            'Input Signal from GPS to activate/deactivate row
OnOff4        var    PortB.5            'Input Signal from GPS to activate/deactivate row                                       

Switch1        var    PortD.0            ''Output to 4066; activates Speed1
Switch2        var    PortE.2            ''Output to 4066; activates Speed2
Switch3        var    PortC.0            ''Output to 4066; activates Speed3
Switch4        var    PortC.3            ''Output to 4066; activates Speed4

MotorSpeed    var    PortC.1            'Input from 4066
Population    var    PortC.2            'Input from GPS

Enable1        var    PortD.1            ''Output Turns on Motor1 driver
Enable2        var    PortD.2            ''Output Turns on Motor2 driver
Enable3        var    PortD.3            ''Output Turns on Motor3 driver
Enable4        var    PortD.4            ''Output Turns on Motor4 driver

SinglePair    var    PortD.7            'Input Determines code path
Input1        var    PortB.0            'PWM0
Input2        var    PortB.1            'PWM1
Input3        var    PortB.2            'PWM2
Input4        var    PortB.3            'PWM3

LCD            var    PortD.5
Duty1          Var    Word
Duty2          Var    Word
Duty3          Var    Word
Duty4          Var    Word
BCD1          var    byte
BCD10          var    byte
Rate          var    word
DisplayTenths  var    word
MotorCount    var    byte              'Tracks motorspeed input
Mod1          var    byte              'Offset tracker to correct motorspeed
Mod2          Var    Byte              'Offset tracker to correct motorspeed
Mod3          var    byte              'Offset tracker to correct motorspeed
Mod4          Var    byte              'Offset tracker to correct motorspeed
PosMin1        var    bit
PosMin2        var    bit
PosMin3        var    bit
PosMin4        var    bit
HighTime      var    word
LowTime        var    word
TotalTime      var    word
Freq          var    word
Prefix          con      $FE            ' needed before each command
LcdCls          CON      $51            ' clear LCD (use PAUSE 5 after)
LcdLine1        CON      $00            ' move cursor to line 1
LcdLine2        con      $40            ' move curson to line 2
LcdLine3        con      $14            ' move curson to line 3
lcdLine4        con      $54            ' move curson to line 4
LcdCol1        con      $00            ' move cursor to column 1
LcdCol2        con      $07            ' move cursor to column 7
Backlight      con      $53            ' Backlighting 1-8
CursorPS        con      $45            'Cursor Position
CursorOn        con      $47            'Cursof On
CursorOff      con      $48            'Cursor Off

INTCON = 0            'Interrupts off for now
INTCON2.7 = 1        'Pull Ups disabled
ADCON0 = 0            'A/D OFF
ANSEL0 = %00000000    'All analogue channels to digital
ANSEL1 = %00000000    'All analogue channels to digital
TRISA = %111111      'PortA to inputs
TRISB = %00010000    'PortB to outputs, except B5
TRISC = %00000110    'PortC, Switch3 and Switch4 outputs; Motorspeed and Population inputs
TRISD = %00000000    'PortD, Switch 1 output; Enable1-4
TRISE = %011
PWMCON0=%01111111    'All odd PWMs enabled, all independent
SSPCON=%00000000      'Disables Serial Port
'DTCON = %00000101      ' ~500nS dead-time (for complementary outputs only)
PTCON0 = %00000010      ' 1:1 postscale, Fosc/4 1:1 prescale, free running mode
Freq=%11111111

PTPERL =0'Freq.LowByte             
PTPERH =1'Freq.HighByte           

PWMCON1 = 1            ' updates enabled, overrides sync w/timebase
PTCON1 = %11000000      ' PWM time base is ON, counts up  500hz
FLTCONFIG = %00000010  ' enable fault A, cycle-by-cycle mode

Serout2 LCD, 84, [Prefix,LcdCLS]
pause 5

         
Test:
Gosub BCD

'Open Loop Motor Control
If BCD1 = 0 then
  'gosub RowControl               
  HIGH Enable1
  HIGH Enable2
  HIGH Enable3
  HIGH Enable4
  pulsin Population, 0, Rate
  Duty1 = (Rate*10)/492      '10%    489
  Duty2 = (Rate*10)/492      '20%    977
  Duty3 = (Rate*10)/492      '50%    2461
  Duty4 = (Rate*10)/492      '80%    3924
  Duty1 = Duty1*10
  Duty2 = Duty2*10
  Duty3 = Duty3*10
  Duty4 = Duty4*10
  PDC0L = Duty4.LowByte
  PDC0H = Duty4.HighByte
  PDC1L = Duty2.LowByte
  PDC1H = Duty2.HighByte
  PDC2L = Duty3.LowByte
  PDC2H = Duty3.HighByte
  PDC3L = Duty1.LowByte
  PDC3H = Duty1.HighByte
  DisplayTenths=Duty1-(Duty1/10*10)
  SEROUT2 LCD,84, [Prefix,CursorPS,0, "Rate ", #Rate, " ", "Duty ", #Duty1/10, ".", #DisplayTenths, "%"]
endif
gosub TEst
BCD:
BCD1=PORTA
BCD1=BCD1 & $0F
BCD1=BCD1^ $0F

'BCD10=PORTC
'BCD10=BCD10 & $F0
'BCD10=BCD10^ $F0
'BCD10 = BCD10 >>4

BCD10=PORTC
BCD10=BCD10 & $0F
BCD10=BCD10^ $0F
return

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I am wondering if its more of a scope deal than code, lol. When I look at a long range of sample points I see a pause. If anyone sees anything wrong with the code I would appreciate any input.

One immediate problem would be the gosub TEst after your IF block. Should be GOTO Test.